Starting phenix.real_space_refine (version: dev) on Thu Dec 22 15:12:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/12_2022/8e4m_27892_trim_updated.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.053 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 49595 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "B" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "C" Number of atoms: 12333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12333 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 776 Unresolved non-hydrogen angles: 980 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "D" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 23.49, per 1000 atoms: 0.47 Number of scatterers: 49595 At special positions: 0 Unit cell: (148.73, 148.73, 147.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 96 16.00 P 16 15.00 O 4636 8.00 N 4307 7.00 C 17036 6.00 H 23500 1.00 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 - 3.50 Amino acid : False - 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: 40.90 Conformation dependent library (CDL) restraints added in 4.7 seconds 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 8 sheets defined 68.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'A' and resid 608 through 635 Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 734 through 757 Processing helix chain 'A' and resid 766 through 786 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 953 through 987 Proline residue: A 958 - end of helix removed outlier: 3.893A pdb=" N PHE A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A1018 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA A1054 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A1070 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1103 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 608 through 635 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 734 through 757 Processing helix chain 'B' and resid 766 through 786 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU B 906 " --> pdb=" O SER B 902 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 953 through 987 Proline residue: B 958 - end of helix removed outlier: 3.893A pdb=" N PHE B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B1018 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA B1054 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B1070 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1103 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE C 165 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 Processing helix chain 'C' and resid 608 through 635 Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 666 through 669 No H-bonds generated for 'chain 'C' and resid 666 through 669' Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 703 through 706' Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 734 through 757 Processing helix chain 'C' and resid 766 through 786 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 807 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE C 858 " --> pdb=" O GLY C 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 869 " --> pdb=" O ILE C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 917 through 921 Processing helix chain 'C' and resid 953 through 987 Proline residue: C 958 - end of helix removed outlier: 3.893A pdb=" N PHE C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C1018 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA C1054 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C1070 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1103 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 521 through 533 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 Processing helix chain 'D' and resid 608 through 635 Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 703 through 706' Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 734 through 757 Processing helix chain 'D' and resid 766 through 786 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 807 " --> pdb=" O THR D 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 808 " --> pdb=" O LEU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE D 858 " --> pdb=" O GLY D 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 869 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 917 through 921 Processing helix chain 'D' and resid 953 through 987 Proline residue: D 958 - end of helix removed outlier: 3.893A pdb=" N PHE D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1024 removed outlier: 5.444A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE D1018 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA D1054 " --> pdb=" O GLU D1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D1070 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 119 Processing sheet with id= B, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS A 326 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 305 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 328 " --> pdb=" O ALA A 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 116 through 119 Processing sheet with id= D, first strand: chain 'B' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS B 326 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA B 305 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 328 " --> pdb=" O ALA B 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 116 through 119 Processing sheet with id= F, first strand: chain 'C' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS C 326 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA C 305 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 328 " --> pdb=" O ALA C 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 116 through 119 Processing sheet with id= H, first strand: chain 'D' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS D 326 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 305 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 328 " --> pdb=" O ALA D 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1636 hydrogen bonds defined for protein. 4560 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: 19.00 Time building geometry restraints manager: 42.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 23456 1.03 - 1.24: 1615 1.24 - 1.44: 10005 1.44 - 1.65: 14899 1.65 - 1.86: 168 Bond restraints: 50143 Sorted by residual: bond pdb=" C5A PIO D1201 " pdb=" C6A PIO D1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO C1201 " pdb=" C6A PIO C1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO A1201 " pdb=" C6A PIO A1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO B1201 " pdb=" C6A PIO B1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C1B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sigma weight residual 1.398 1.448 -0.050 2.00e-02 2.50e+03 6.16e+00 ... (remaining 50138 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 642 106.97 - 113.74: 56505 113.74 - 120.50: 17961 120.50 - 127.26: 14381 127.26 - 134.03: 292 Bond angle restraints: 89781 Sorted by residual: angle pdb=" C ILE B 701 " pdb=" N ILE B 702 " pdb=" CA ILE B 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE C 701 " pdb=" N ILE C 702 " pdb=" CA ILE C 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE D 701 " pdb=" N ILE D 702 " pdb=" CA ILE D 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" N ILE D 403 " pdb=" CA ILE D 403 " pdb=" C ILE D 403 " ideal model delta sigma weight residual 111.90 109.30 2.60 8.10e-01 1.52e+00 1.03e+01 ... (remaining 89776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 19074 15.02 - 30.03: 1044 30.03 - 45.05: 232 45.05 - 60.07: 56 60.07 - 75.08: 20 Dihedral angle restraints: 20426 sinusoidal: 7964 harmonic: 12462 Sorted by residual: dihedral pdb=" CA GLY C 708 " pdb=" C GLY C 708 " pdb=" N LEU C 709 " pdb=" CA LEU C 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY A 708 " pdb=" C GLY A 708 " pdb=" N LEU A 709 " pdb=" CA LEU A 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY D 708 " pdb=" C GLY D 708 " pdb=" N LEU D 709 " pdb=" CA LEU D 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 20423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3400 0.035 - 0.070: 654 0.070 - 0.105: 212 0.105 - 0.141: 53 0.141 - 0.176: 4 Chirality restraints: 4323 Sorted by residual: chirality pdb=" CA THR D 982 " pdb=" N THR D 982 " pdb=" C THR D 982 " pdb=" CB THR D 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA THR C 982 " pdb=" N THR C 982 " pdb=" C THR C 982 " pdb=" CB THR C 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA THR B 982 " pdb=" N THR B 982 " pdb=" C THR B 982 " pdb=" CB THR B 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 4320 not shown) Planarity restraints: 7884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 982 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C THR B 982 " -0.047 2.00e-02 2.50e+03 pdb=" O THR B 982 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL B 983 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 982 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C THR A 982 " -0.047 2.00e-02 2.50e+03 pdb=" O THR A 982 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 983 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 982 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C THR C 982 " 0.047 2.00e-02 2.50e+03 pdb=" O THR C 982 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL C 983 " -0.016 2.00e-02 2.50e+03 ... (remaining 7881 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2521 2.20 - 2.80: 98557 2.80 - 3.40: 131547 3.40 - 4.00: 162144 4.00 - 4.60: 255198 Nonbonded interactions: 649967 Sorted by model distance: nonbonded pdb=" O GLY C 684 " pdb="HH22 ARG C 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY D 684 " pdb="HH22 ARG D 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY A 684 " pdb="HH22 ARG A 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY B 684 " pdb="HH22 ARG B 713 " model vdw 1.603 1.850 nonbonded pdb=" HG1 THR A 494 " pdb=" O PHE A 531 " model vdw 1.615 1.850 ... (remaining 649962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) selection = (chain 'B' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) selection = chain 'C' selection = (chain 'D' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 16 5.49 5 S 96 5.16 5 C 17036 2.51 5 N 4307 2.21 5 O 4636 1.98 5 H 23500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.850 Extract box with map and model: 8.530 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.420 Process input model: 151.150 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.003 0.052 26643 Z= 0.195 Angle : 0.448 5.349 36358 Z= 0.253 Chirality : 0.034 0.176 4323 Planarity : 0.003 0.058 4496 Dihedral : 10.684 75.085 8588 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.00 % 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: 3.12 (0.15), residues: 3404 helix: 2.91 (0.11), residues: 2516 sheet: 0.74 (0.38), residues: 176 loop : -0.85 (0.24), residues: 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 612 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.7135 time to fit residues: 704.1705 Evaluate side-chains 397 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 3.9990 chunk 266 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN B 681 GLN C 681 GLN D 681 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 26643 Z= 0.538 Angle : 0.664 6.189 36358 Z= 0.367 Chirality : 0.041 0.176 4323 Planarity : 0.005 0.058 4496 Dihedral : 7.219 73.267 3780 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.86 % 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: 1.74 (0.15), residues: 3404 helix: 1.92 (0.10), residues: 2472 sheet: -0.00 (0.35), residues: 176 loop : -1.12 (0.24), residues: 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 380 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 43 residues processed: 420 average time/residue: 0.7704 time to fit residues: 530.0224 Evaluate side-chains 390 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 347 time to evaluate : 4.178 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6904 time to fit residues: 54.8262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 88 optimal weight: 40.0000 chunk 320 optimal weight: 0.8980 chunk 345 optimal weight: 0.8980 chunk 285 optimal weight: 20.0000 chunk 317 optimal weight: 0.0010 chunk 109 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 26643 Z= 0.149 Angle : 0.466 6.066 36358 Z= 0.249 Chirality : 0.034 0.141 4323 Planarity : 0.004 0.058 4496 Dihedral : 6.548 70.085 3780 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.21 % 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: 2.41 (0.15), residues: 3404 helix: 2.47 (0.11), residues: 2469 sheet: 0.27 (0.35), residues: 176 loop : -1.11 (0.24), residues: 759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 4.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 376 average time/residue: 0.7648 time to fit residues: 473.1836 Evaluate side-chains 343 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 4.253 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5438 time to fit residues: 10.2573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.5980 chunk 240 optimal weight: 40.0000 chunk 166 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 152 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 340 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 26643 Z= 0.221 Angle : 0.471 5.406 36358 Z= 0.254 Chirality : 0.034 0.146 4323 Planarity : 0.004 0.058 4496 Dihedral : 6.254 68.308 3780 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.98 % 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: 2.41 (0.15), residues: 3404 helix: 2.46 (0.11), residues: 2480 sheet: 0.13 (0.34), residues: 176 loop : -1.11 (0.24), residues: 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 343 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 355 average time/residue: 0.7298 time to fit residues: 432.0392 Evaluate side-chains 330 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 322 time to evaluate : 4.222 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5128 time to fit residues: 13.0460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.1980 chunk 193 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 173 optimal weight: 40.0000 chunk 305 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 26643 Z= 0.150 Angle : 0.448 5.793 36358 Z= 0.239 Chirality : 0.034 0.145 4323 Planarity : 0.004 0.057 4496 Dihedral : 6.050 71.406 3780 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.51 % 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 (0.15), residues: 3404 helix: 2.59 (0.11), residues: 2484 sheet: 0.16 (0.34), residues: 176 loop : -1.17 (0.24), residues: 744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 355 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 355 average time/residue: 0.6898 time to fit residues: 407.0545 Evaluate side-chains 342 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 335 time to evaluate : 4.073 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5344 time to fit residues: 11.7720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 178 optimal weight: 30.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 26643 Z= 0.341 Angle : 0.509 5.551 36358 Z= 0.280 Chirality : 0.036 0.145 4323 Planarity : 0.004 0.057 4496 Dihedral : 6.150 71.660 3780 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.38 % 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: 2.19 (0.15), residues: 3404 helix: 2.36 (0.11), residues: 2460 sheet: -0.09 (0.33), residues: 176 loop : -1.29 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 335 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 339 average time/residue: 0.7658 time to fit residues: 435.2333 Evaluate side-chains 317 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5822 time to fit residues: 10.9049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 192 optimal weight: 0.1980 chunk 286 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 339 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 26643 Z= 0.184 Angle : 0.460 5.877 36358 Z= 0.245 Chirality : 0.034 0.145 4323 Planarity : 0.004 0.057 4496 Dihedral : 5.914 71.571 3780 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.47 % 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: 2.46 (0.15), residues: 3404 helix: 2.56 (0.11), residues: 2464 sheet: -0.03 (0.34), residues: 176 loop : -1.21 (0.23), residues: 764 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 355 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 363 average time/residue: 0.6987 time to fit residues: 422.3894 Evaluate side-chains 348 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 345 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6204 time to fit residues: 8.6979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 266 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 26643 Z= 0.327 Angle : 0.517 7.788 36358 Z= 0.279 Chirality : 0.036 0.144 4323 Planarity : 0.004 0.058 4496 Dihedral : 5.997 67.045 3780 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.73 % 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: 2.19 (0.15), residues: 3404 helix: 2.38 (0.11), residues: 2456 sheet: -0.21 (0.34), residues: 176 loop : -1.29 (0.23), residues: 772 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 353 average time/residue: 0.7203 time to fit residues: 426.9841 Evaluate side-chains 334 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 321 time to evaluate : 4.277 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5256 time to fit residues: 18.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 5.9990 chunk 325 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 299 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26643 Z= 0.218 Angle : 0.490 9.580 36358 Z= 0.259 Chirality : 0.035 0.142 4323 Planarity : 0.004 0.055 4496 Dihedral : 5.907 63.880 3780 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.60 % 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: 2.28 (0.15), residues: 3404 helix: 2.42 (0.11), residues: 2464 sheet: -0.20 (0.35), residues: 176 loop : -1.21 (0.24), residues: 764 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 341 time to evaluate : 4.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 14 residues processed: 344 average time/residue: 0.7258 time to fit residues: 414.9476 Evaluate side-chains 339 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 325 time to evaluate : 3.980 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5445 time to fit residues: 18.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 350 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 26643 Z= 0.167 Angle : 0.478 9.025 36358 Z= 0.250 Chirality : 0.035 0.139 4323 Planarity : 0.004 0.055 4496 Dihedral : 5.853 63.842 3780 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.00 % 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: 2.43 (0.15), residues: 3404 helix: 2.54 (0.11), residues: 2464 sheet: -0.01 (0.35), residues: 176 loop : -1.21 (0.24), residues: 764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.7299 time to fit residues: 402.8248 Evaluate side-chains 322 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 4.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 257 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.156218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107787 restraints weight = 148057.595| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.04 r_work: 0.3283 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 26643 Z= 0.194 Angle : 0.482 8.490 36358 Z= 0.252 Chirality : 0.035 0.143 4323 Planarity : 0.004 0.055 4496 Dihedral : 5.779 64.570 3780 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.00 % 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: 2.47 (0.15), residues: 3404 helix: 2.56 (0.11), residues: 2468 sheet: -0.05 (0.35), residues: 176 loop : -1.19 (0.23), residues: 760 =============================================================================== Job complete usr+sys time: 9800.60 seconds wall clock time: 173 minutes 59.44 seconds (10439.44 seconds total)