Starting phenix.real_space_refine on Sun Apr 14 05:01:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrd_32723/04_2024/7wrd_32723_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 851": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 784": "NH1" <-> "NH2" Residue "C ARG 816": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "C ARG 885": "NH1" <-> "NH2" Residue "C PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 784": "NH1" <-> "NH2" Residue "D ARG 816": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 851": "NH1" <-> "NH2" Residue "D ARG 885": "NH1" <-> "NH2" Residue "D PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.72, per 1000 atoms: 0.52 Number of scatterers: 30468 At special positions: 0 Unit cell: (153.114, 153.114, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 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: 12.17 Conformation dependent library (CDL) restraints added in 5.5 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 4 sheets defined 63.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.93 Creating SS restraints... Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.730A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 361 removed outlier: 3.561A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 removed outlier: 4.216A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 371 through 385 removed outlier: 4.120A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.681A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 471 through 480 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 498 Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.932A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 3.991A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.831A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 4.416A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 789 Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 797 through 816 Processing helix chain 'A' and resid 822 through 849 removed outlier: 4.205A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 889 removed outlier: 3.955A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 3.880A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 911 removed outlier: 4.109A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 953 through 968 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 970 through 1006 removed outlier: 3.656A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1029 removed outlier: 4.912A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.891A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1103 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.731A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 361 removed outlier: 3.561A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 removed outlier: 4.216A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 371 through 385 removed outlier: 4.120A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.680A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 471 through 480 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 498 Processing helix chain 'B' and resid 504 through 515 Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 576 through 583 removed outlier: 3.933A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 603 removed outlier: 3.991A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.830A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 removed outlier: 4.416A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 789 Processing helix chain 'B' and resid 792 through 795 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 822 through 849 removed outlier: 4.206A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 889 removed outlier: 3.955A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 862 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET B 863 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU B 864 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 903 removed outlier: 3.880A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 911 removed outlier: 4.109A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 953 through 968 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 970 through 1006 removed outlier: 3.657A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 977 " --> pdb=" O ASN B 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1029 removed outlier: 4.913A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1070 removed outlier: 3.891A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1103 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 159 through 175 Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.730A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 361 removed outlier: 3.562A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 removed outlier: 4.216A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 371 through 385 removed outlier: 4.119A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.681A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 471 through 480 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 498 Processing helix chain 'C' and resid 504 through 515 Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 576 through 583 removed outlier: 3.933A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 603 removed outlier: 3.991A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.830A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 645 removed outlier: 4.416A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 702 through 704 No H-bonds generated for 'chain 'C' and resid 702 through 704' Processing helix chain 'C' and resid 724 through 731 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 789 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 797 through 816 Processing helix chain 'C' and resid 822 through 849 removed outlier: 4.206A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 889 removed outlier: 3.954A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET C 863 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 864 " --> pdb=" O LEU C 860 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP C 866 " --> pdb=" O ARG C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 903 removed outlier: 3.880A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 911 removed outlier: 4.109A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 953 through 968 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 970 through 1006 removed outlier: 3.657A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 977 " --> pdb=" O ASN C 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1029 removed outlier: 4.913A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1070 removed outlier: 3.891A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1103 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.731A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 361 removed outlier: 3.562A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 removed outlier: 4.217A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 368' Processing helix chain 'D' and resid 371 through 385 removed outlier: 4.119A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 removed outlier: 3.680A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 435 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 471 through 480 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 498 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 519 through 531 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 576 through 583 removed outlier: 3.933A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 603 removed outlier: 3.991A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.830A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 645 removed outlier: 4.416A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 702 through 704 No H-bonds generated for 'chain 'D' and resid 702 through 704' Processing helix chain 'D' and resid 724 through 731 Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 789 Processing helix chain 'D' and resid 792 through 795 Processing helix chain 'D' and resid 797 through 816 Processing helix chain 'D' and resid 822 through 849 removed outlier: 4.206A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 889 removed outlier: 3.954A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG D 862 " --> pdb=" O ILE D 858 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET D 863 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 903 removed outlier: 3.882A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 911 removed outlier: 4.109A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 953 through 968 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 970 through 1006 removed outlier: 3.656A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 977 " --> pdb=" O ASN D 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1029 removed outlier: 4.912A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1070 removed outlier: 3.891A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 119 through 121 removed outlier: 7.905A pdb=" N LEU A 120 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 262 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 119 through 121 removed outlier: 7.906A pdb=" N LEU B 120 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU B 262 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 119 through 121 removed outlier: 7.905A pdb=" N LEU C 120 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU C 262 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 119 through 121 removed outlier: 7.905A pdb=" N LEU D 120 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU D 262 " --> pdb=" O LEU D 120 " (cutoff:3.500A) 1612 hydrogen bonds defined for protein. 4656 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: 11.36 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4884 1.30 - 1.43: 8700 1.43 - 1.56: 17388 1.56 - 1.69: 4 1.69 - 1.82: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.396 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.396 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.48e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.09: 275 104.09 - 111.60: 13186 111.60 - 119.11: 12260 119.11 - 126.62: 16003 126.62 - 134.13: 528 Bond angle restraints: 42252 Sorted by residual: angle pdb=" C ILE C1011 " pdb=" N PRO C1012 " pdb=" CA PRO C1012 " ideal model delta sigma weight residual 119.78 127.01 -7.23 1.03e+00 9.43e-01 4.93e+01 angle pdb=" C ILE D1011 " pdb=" N PRO D1012 " pdb=" CA PRO D1012 " ideal model delta sigma weight residual 119.78 126.99 -7.21 1.03e+00 9.43e-01 4.91e+01 angle pdb=" C ILE B1011 " pdb=" N PRO B1012 " pdb=" CA PRO B1012 " ideal model delta sigma weight residual 119.78 126.96 -7.18 1.03e+00 9.43e-01 4.85e+01 angle pdb=" C ILE A1011 " pdb=" N PRO A1012 " pdb=" CA PRO A1012 " ideal model delta sigma weight residual 119.78 126.95 -7.17 1.03e+00 9.43e-01 4.84e+01 angle pdb=" N LEU C 704 " pdb=" CA LEU C 704 " pdb=" C LEU C 704 " ideal model delta sigma weight residual 113.16 107.07 6.09 1.24e+00 6.50e-01 2.41e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 17135 15.01 - 30.03: 886 30.03 - 45.04: 239 45.04 - 60.05: 12 60.05 - 75.07: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B 916 " pdb=" C PRO B 916 " pdb=" N SER B 917 " pdb=" CA SER B 917 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PRO C 916 " pdb=" C PRO C 916 " pdb=" N SER C 917 " pdb=" CA SER C 917 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO A 916 " pdb=" C PRO A 916 " pdb=" N SER A 917 " pdb=" CA SER A 917 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2933 0.049 - 0.099: 1359 0.099 - 0.148: 308 0.148 - 0.197: 88 0.197 - 0.246: 20 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ILE B 324 " pdb=" N ILE B 324 " pdb=" C ILE B 324 " pdb=" CB ILE B 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 324 " pdb=" N ILE C 324 " pdb=" C ILE C 324 " pdb=" CB ILE C 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ILE A 324 " pdb=" N ILE A 324 " pdb=" C ILE A 324 " pdb=" CB ILE A 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 454 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLU D 454 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU D 454 " -0.027 2.00e-02 2.50e+03 pdb=" N SER D 455 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 454 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C GLU B 454 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU B 454 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 455 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 454 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C GLU A 454 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU A 454 " 0.027 2.00e-02 2.50e+03 pdb=" N SER A 455 " 0.024 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6415 2.77 - 3.31: 28331 3.31 - 3.84: 48780 3.84 - 4.37: 57717 4.37 - 4.90: 97933 Nonbonded interactions: 239176 Sorted by model distance: nonbonded pdb=" O VAL C 728 " pdb=" OG1 THR C 732 " model vdw 2.242 2.440 nonbonded pdb=" O VAL B 728 " pdb=" OG1 THR B 732 " model vdw 2.243 2.440 nonbonded pdb=" O VAL A 728 " pdb=" OG1 THR A 732 " model vdw 2.243 2.440 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.243 2.440 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.250 2.440 ... (remaining 239171 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.020 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 81.220 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.009 0.189 31188 Z= 0.582 Angle : 1.079 10.386 42252 Z= 0.600 Chirality : 0.059 0.246 4708 Planarity : 0.007 0.066 5280 Dihedral : 10.611 75.066 11212 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.80 % Favored : 93.98 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.61 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2396 sheet: -1.88 (0.33), residues: 200 loop : -2.92 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP B 740 HIS 0.010 0.003 HIS A 845 PHE 0.037 0.004 PHE B 832 TYR 0.040 0.004 TYR A 772 ARG 0.009 0.001 ARG C 829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 770 time to evaluate : 3.526 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: A 190 LYS cc_start: 0.8642 (ttmm) cc_final: 0.7897 (ttmm) REVERT: A 277 LEU cc_start: 0.8180 (tp) cc_final: 0.7924 (tm) REVERT: A 464 THR cc_start: 0.8764 (m) cc_final: 0.8541 (p) REVERT: A 510 GLN cc_start: 0.7819 (mt0) cc_final: 0.7517 (mt0) REVERT: A 758 MET cc_start: 0.8681 (mtp) cc_final: 0.8410 (mtm) REVERT: A 1026 LYS cc_start: 0.5441 (tmmt) cc_final: 0.5079 (mptm) REVERT: B 190 LYS cc_start: 0.8635 (ttmm) cc_final: 0.7893 (ttmm) REVERT: B 277 LEU cc_start: 0.8178 (tp) cc_final: 0.7929 (tm) REVERT: B 464 THR cc_start: 0.8767 (m) cc_final: 0.8542 (p) REVERT: B 510 GLN cc_start: 0.7822 (mt0) cc_final: 0.7520 (mt0) REVERT: B 758 MET cc_start: 0.8682 (mtp) cc_final: 0.8417 (mtm) REVERT: B 1026 LYS cc_start: 0.5441 (tmmt) cc_final: 0.5079 (mptm) REVERT: C 190 LYS cc_start: 0.8635 (ttmm) cc_final: 0.7895 (ttmm) REVERT: C 277 LEU cc_start: 0.8180 (tp) cc_final: 0.7927 (tm) REVERT: C 337 ASP cc_start: 0.7104 (m-30) cc_final: 0.6892 (t0) REVERT: C 464 THR cc_start: 0.8768 (m) cc_final: 0.8543 (p) REVERT: C 510 GLN cc_start: 0.7818 (mt0) cc_final: 0.7513 (mt0) REVERT: C 758 MET cc_start: 0.8685 (mtp) cc_final: 0.8417 (mtm) REVERT: C 1026 LYS cc_start: 0.5418 (tmmt) cc_final: 0.5059 (mptm) REVERT: D 190 LYS cc_start: 0.8642 (ttmm) cc_final: 0.7899 (ttmm) REVERT: D 277 LEU cc_start: 0.8185 (tp) cc_final: 0.7930 (tm) REVERT: D 337 ASP cc_start: 0.7116 (m-30) cc_final: 0.6897 (t0) REVERT: D 464 THR cc_start: 0.8769 (m) cc_final: 0.8543 (p) REVERT: D 510 GLN cc_start: 0.7817 (mt0) cc_final: 0.7519 (mt0) REVERT: D 758 MET cc_start: 0.8682 (mtp) cc_final: 0.8410 (mtm) REVERT: D 1026 LYS cc_start: 0.5429 (tmmt) cc_final: 0.5070 (mptm) outliers start: 4 outliers final: 0 residues processed: 774 average time/residue: 1.5624 time to fit residues: 1404.2434 Evaluate side-chains 375 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 0.0050 chunk 337 optimal weight: 0.9980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 279 ASN A 666 GLN A 671 GLN A 675 GLN A 861 GLN A 987 GLN A1050 ASN B 199 ASN B 279 ASN B 666 GLN B 671 GLN B 675 GLN B 861 GLN B 987 GLN B1050 ASN C 199 ASN C 279 ASN C 666 GLN C 671 GLN C 675 GLN C 861 GLN C 987 GLN C1050 ASN C1074 ASN D 199 ASN D 279 ASN D 666 GLN D 671 GLN D 675 GLN D 861 GLN D 987 GLN D1050 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31188 Z= 0.202 Angle : 0.620 7.942 42252 Z= 0.322 Chirality : 0.040 0.136 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.927 56.777 4024 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.22 % Allowed : 13.64 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.13), residues: 3656 helix: -0.18 (0.10), residues: 2436 sheet: -1.36 (0.34), residues: 200 loop : -2.66 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 898 HIS 0.004 0.001 HIS C 138 PHE 0.018 0.001 PHE B 752 TYR 0.016 0.002 TYR A 191 ARG 0.006 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 452 time to evaluate : 3.927 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: A 190 LYS cc_start: 0.8523 (ttmm) cc_final: 0.7837 (ttmm) REVERT: A 292 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6448 (p0) REVERT: A 396 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6241 (mpp) REVERT: A 402 GLU cc_start: 0.7260 (pp20) cc_final: 0.7036 (pp20) REVERT: A 574 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7913 (tppt) REVERT: A 758 MET cc_start: 0.8642 (mtp) cc_final: 0.8390 (mtm) REVERT: A 989 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7451 (t0) REVERT: A 1023 MET cc_start: 0.6862 (mmm) cc_final: 0.4989 (ttm) REVERT: A 1026 LYS cc_start: 0.5542 (tmmt) cc_final: 0.5208 (mptm) REVERT: B 123 ASP cc_start: 0.6531 (m-30) cc_final: 0.5865 (p0) REVERT: B 190 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7834 (ttmm) REVERT: B 292 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6450 (p0) REVERT: B 396 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6248 (mpp) REVERT: B 402 GLU cc_start: 0.7262 (pp20) cc_final: 0.7054 (pp20) REVERT: B 758 MET cc_start: 0.8643 (mtp) cc_final: 0.8394 (mtm) REVERT: B 988 GLU cc_start: 0.7141 (pm20) cc_final: 0.6941 (pm20) REVERT: B 989 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7451 (t0) REVERT: B 1023 MET cc_start: 0.6801 (mmm) cc_final: 0.4957 (ttm) REVERT: B 1026 LYS cc_start: 0.5545 (tmmt) cc_final: 0.5210 (mptm) REVERT: C 123 ASP cc_start: 0.6541 (m-30) cc_final: 0.5872 (p0) REVERT: C 190 LYS cc_start: 0.8499 (ttmm) cc_final: 0.7817 (ttmm) REVERT: C 292 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6450 (p0) REVERT: C 396 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6242 (mpp) REVERT: C 402 GLU cc_start: 0.7260 (pp20) cc_final: 0.7050 (pp20) REVERT: C 758 MET cc_start: 0.8644 (mtp) cc_final: 0.8391 (mtm) REVERT: C 988 GLU cc_start: 0.7148 (pm20) cc_final: 0.6948 (pm20) REVERT: C 989 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7453 (t0) REVERT: C 1023 MET cc_start: 0.6838 (mmm) cc_final: 0.4971 (ttm) REVERT: C 1026 LYS cc_start: 0.5516 (tmmt) cc_final: 0.5185 (mptm) REVERT: D 123 ASP cc_start: 0.6533 (m-30) cc_final: 0.5866 (p0) REVERT: D 190 LYS cc_start: 0.8505 (ttmm) cc_final: 0.7820 (ttmm) REVERT: D 292 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6448 (p0) REVERT: D 396 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6243 (mpp) REVERT: D 402 GLU cc_start: 0.7268 (pp20) cc_final: 0.7056 (pp20) REVERT: D 758 MET cc_start: 0.8642 (mtp) cc_final: 0.8387 (mtm) REVERT: D 989 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7456 (t0) REVERT: D 1023 MET cc_start: 0.6839 (mmm) cc_final: 0.4974 (ttm) REVERT: D 1026 LYS cc_start: 0.5531 (tmmt) cc_final: 0.5196 (mptm) outliers start: 107 outliers final: 24 residues processed: 527 average time/residue: 1.5128 time to fit residues: 931.3556 Evaluate side-chains 389 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 352 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 0.0970 chunk 281 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 5.9990 chunk 365 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS A 572 ASN A 666 GLN A 741 ASN A1074 ASN B 259 HIS B 438 GLN B 572 ASN B 666 GLN B 741 ASN B 886 GLN B1074 ASN C 259 HIS C 438 GLN C 572 ASN C 666 GLN C 741 ASN C 886 GLN D 259 HIS D 572 ASN D 666 GLN D 741 ASN D 886 GLN D1074 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31188 Z= 0.335 Angle : 0.681 7.811 42252 Z= 0.351 Chirality : 0.043 0.133 4708 Planarity : 0.005 0.042 5280 Dihedral : 5.796 57.181 4024 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.33 % Allowed : 14.45 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3656 helix: 0.36 (0.10), residues: 2428 sheet: -1.31 (0.34), residues: 200 loop : -2.48 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 798 HIS 0.005 0.001 HIS A 765 PHE 0.030 0.002 PHE A 752 TYR 0.016 0.002 TYR D 772 ARG 0.006 0.001 ARG A1079 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 381 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8297 (ptmt) REVERT: A 294 ASN cc_start: 0.8134 (p0) cc_final: 0.7867 (p0) REVERT: A 364 ARG cc_start: 0.6816 (ttm170) cc_final: 0.6176 (tpm170) REVERT: A 402 GLU cc_start: 0.7378 (pp20) cc_final: 0.7140 (pp20) REVERT: A 585 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6807 (mttt) REVERT: A 689 ASP cc_start: 0.7121 (p0) cc_final: 0.6825 (p0) REVERT: A 802 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: A 804 LEU cc_start: 0.8737 (tp) cc_final: 0.8491 (mt) REVERT: A 897 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7356 (mmt180) REVERT: A 988 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: A 989 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7507 (t0) REVERT: A 1026 LYS cc_start: 0.5582 (tmmt) cc_final: 0.5266 (mptm) REVERT: B 123 ASP cc_start: 0.6786 (m-30) cc_final: 0.5964 (p0) REVERT: B 163 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8292 (ptmt) REVERT: B 190 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8309 (ptmt) REVERT: B 294 ASN cc_start: 0.8129 (p0) cc_final: 0.7864 (p0) REVERT: B 402 GLU cc_start: 0.7363 (pp20) cc_final: 0.7145 (pp20) REVERT: B 585 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6803 (mttt) REVERT: B 689 ASP cc_start: 0.7123 (p0) cc_final: 0.6832 (p0) REVERT: B 802 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: B 804 LEU cc_start: 0.8747 (tp) cc_final: 0.8499 (mt) REVERT: B 897 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7359 (mmt180) REVERT: B 1026 LYS cc_start: 0.5500 (tmmt) cc_final: 0.5204 (mptm) REVERT: C 123 ASP cc_start: 0.6797 (m-30) cc_final: 0.5967 (p0) REVERT: C 163 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8296 (ptmt) REVERT: C 190 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8307 (ptmt) REVERT: C 294 ASN cc_start: 0.8122 (p0) cc_final: 0.7845 (p0) REVERT: C 402 GLU cc_start: 0.7361 (pp20) cc_final: 0.7136 (pp20) REVERT: C 585 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6801 (mttt) REVERT: C 689 ASP cc_start: 0.7125 (p0) cc_final: 0.6833 (p0) REVERT: C 802 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: C 804 LEU cc_start: 0.8744 (tp) cc_final: 0.8497 (mt) REVERT: C 897 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7360 (mmt180) REVERT: C 1023 MET cc_start: 0.6870 (mmm) cc_final: 0.4909 (ttm) REVERT: C 1026 LYS cc_start: 0.5470 (tmmt) cc_final: 0.5191 (mptm) REVERT: D 123 ASP cc_start: 0.6787 (m-30) cc_final: 0.5960 (p0) REVERT: D 163 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8294 (ptmt) REVERT: D 190 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8312 (ptmt) REVERT: D 294 ASN cc_start: 0.8135 (p0) cc_final: 0.7860 (p0) REVERT: D 402 GLU cc_start: 0.7377 (pp20) cc_final: 0.7153 (pp20) REVERT: D 585 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6806 (mttt) REVERT: D 689 ASP cc_start: 0.7118 (p0) cc_final: 0.6828 (p0) REVERT: D 802 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: D 804 LEU cc_start: 0.8743 (tp) cc_final: 0.8497 (mt) REVERT: D 897 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7358 (mmt180) REVERT: D 988 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: D 989 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7504 (t0) REVERT: D 1023 MET cc_start: 0.6866 (mmm) cc_final: 0.4909 (ttm) REVERT: D 1026 LYS cc_start: 0.5485 (tmmt) cc_final: 0.5201 (mptm) outliers start: 144 outliers final: 64 residues processed: 480 average time/residue: 1.4533 time to fit residues: 822.2442 Evaluate side-chains 419 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 359 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 321 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN A 671 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 671 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 671 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 666 GLN D 671 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31188 Z= 0.173 Angle : 0.565 6.628 42252 Z= 0.289 Chirality : 0.039 0.152 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.345 52.110 4024 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.28 % Allowed : 16.50 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3656 helix: 0.89 (0.11), residues: 2436 sheet: -1.18 (0.35), residues: 200 loop : -2.28 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 786 HIS 0.002 0.001 HIS C 138 PHE 0.012 0.001 PHE C 165 TYR 0.029 0.001 TYR C 191 ARG 0.007 0.000 ARG C1079 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 424 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8173 (ptmt) REVERT: A 201 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8021 (tp) REVERT: A 292 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6654 (p0) REVERT: A 294 ASN cc_start: 0.8052 (p0) cc_final: 0.7768 (p0) REVERT: A 364 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5959 (OUTLIER) REVERT: A 402 GLU cc_start: 0.7399 (pp20) cc_final: 0.7006 (pp20) REVERT: A 627 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 689 ASP cc_start: 0.7014 (p0) cc_final: 0.6698 (p0) REVERT: A 758 MET cc_start: 0.8670 (mtp) cc_final: 0.8398 (mtm) REVERT: A 797 LEU cc_start: 0.7091 (pt) cc_final: 0.6799 (mt) REVERT: A 804 LEU cc_start: 0.8613 (tp) cc_final: 0.8375 (mt) REVERT: A 863 MET cc_start: 0.8035 (mmt) cc_final: 0.7591 (mmt) REVERT: A 897 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7200 (mmt180) REVERT: A 953 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 988 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6094 (pm20) REVERT: A 989 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7385 (t0) REVERT: A 1023 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.4817 (ttm) REVERT: A 1026 LYS cc_start: 0.5680 (tmmt) cc_final: 0.5356 (mptm) REVERT: B 123 ASP cc_start: 0.6693 (m-30) cc_final: 0.5932 (p0) REVERT: B 163 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8170 (ptmt) REVERT: B 201 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 292 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6599 (p0) REVERT: B 294 ASN cc_start: 0.8051 (p0) cc_final: 0.7767 (p0) REVERT: B 364 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6218 (tpm170) REVERT: B 402 GLU cc_start: 0.7368 (pp20) cc_final: 0.6979 (pp20) REVERT: B 574 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7300 (tppt) REVERT: B 620 GLU cc_start: 0.7133 (tt0) cc_final: 0.6471 (tt0) REVERT: B 627 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: B 689 ASP cc_start: 0.7036 (p0) cc_final: 0.6722 (p0) REVERT: B 758 MET cc_start: 0.8674 (mtp) cc_final: 0.8397 (mtm) REVERT: B 797 LEU cc_start: 0.7103 (pt) cc_final: 0.6798 (mt) REVERT: B 804 LEU cc_start: 0.8621 (tp) cc_final: 0.8381 (mt) REVERT: B 863 MET cc_start: 0.8045 (mmt) cc_final: 0.7611 (mmt) REVERT: B 897 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7203 (mmt180) REVERT: B 953 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 1023 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.4765 (ttm) REVERT: B 1026 LYS cc_start: 0.5683 (tmmt) cc_final: 0.5361 (mptm) REVERT: C 123 ASP cc_start: 0.6705 (m-30) cc_final: 0.5936 (p0) REVERT: C 163 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8176 (ptmt) REVERT: C 201 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8033 (tp) REVERT: C 292 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6603 (p0) REVERT: C 294 ASN cc_start: 0.8041 (p0) cc_final: 0.7749 (p0) REVERT: C 364 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6220 (tpm170) REVERT: C 402 GLU cc_start: 0.7368 (pp20) cc_final: 0.6973 (pp20) REVERT: C 574 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7302 (tppt) REVERT: C 620 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: C 627 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: C 689 ASP cc_start: 0.7032 (p0) cc_final: 0.6718 (p0) REVERT: C 758 MET cc_start: 0.8670 (mtp) cc_final: 0.8396 (mtm) REVERT: C 797 LEU cc_start: 0.7099 (pt) cc_final: 0.6754 (mt) REVERT: C 804 LEU cc_start: 0.8612 (tp) cc_final: 0.8377 (mt) REVERT: C 863 MET cc_start: 0.8037 (mmt) cc_final: 0.7597 (mmt) REVERT: C 897 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7204 (mmt180) REVERT: C 953 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 1023 MET cc_start: 0.6700 (mmm) cc_final: 0.4868 (ttm) REVERT: C 1026 LYS cc_start: 0.5574 (tmmt) cc_final: 0.5277 (mptm) REVERT: D 123 ASP cc_start: 0.6692 (m-30) cc_final: 0.5928 (p0) REVERT: D 163 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8171 (ptmt) REVERT: D 201 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8034 (tp) REVERT: D 292 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6484 (p0) REVERT: D 294 ASN cc_start: 0.8045 (p0) cc_final: 0.7751 (p0) REVERT: D 364 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6221 (tpm170) REVERT: D 402 GLU cc_start: 0.7380 (pp20) cc_final: 0.6980 (pp20) REVERT: D 574 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7303 (tppt) REVERT: D 620 GLU cc_start: 0.7145 (tt0) cc_final: 0.6484 (tt0) REVERT: D 627 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: D 689 ASP cc_start: 0.7024 (p0) cc_final: 0.6706 (p0) REVERT: D 758 MET cc_start: 0.8669 (mtp) cc_final: 0.8397 (mtm) REVERT: D 797 LEU cc_start: 0.7094 (pt) cc_final: 0.6796 (mt) REVERT: D 804 LEU cc_start: 0.8617 (tp) cc_final: 0.8383 (mt) REVERT: D 863 MET cc_start: 0.8031 (mmt) cc_final: 0.7590 (mmt) REVERT: D 897 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7202 (mmt180) REVERT: D 953 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7198 (mt-10) REVERT: D 988 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6169 (pm20) REVERT: D 989 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7358 (t0) REVERT: D 1023 MET cc_start: 0.6689 (mmm) cc_final: 0.4840 (ttm) REVERT: D 1026 LYS cc_start: 0.5585 (tmmt) cc_final: 0.5283 (mptm) outliers start: 109 outliers final: 44 residues processed: 499 average time/residue: 1.5760 time to fit residues: 916.6621 Evaluate side-chains 415 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 346 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 306 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN B 154 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN C 154 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN D 154 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31188 Z= 0.270 Angle : 0.627 8.180 42252 Z= 0.319 Chirality : 0.041 0.131 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.282 52.425 4024 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.85 % Allowed : 18.00 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3656 helix: 0.91 (0.11), residues: 2432 sheet: -1.22 (0.34), residues: 200 loop : -2.17 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 786 HIS 0.005 0.001 HIS C 845 PHE 0.017 0.002 PHE B 752 TYR 0.020 0.002 TYR A 191 ARG 0.007 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 351 time to evaluate : 3.774 Fit side-chains REVERT: A 146 ILE cc_start: 0.8624 (mt) cc_final: 0.8362 (tt) REVERT: A 153 LYS cc_start: 0.5711 (pttt) cc_final: 0.5256 (pmtt) REVERT: A 163 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8239 (ptmt) REVERT: A 292 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6642 (p0) REVERT: A 294 ASN cc_start: 0.8078 (p0) cc_final: 0.7774 (p0) REVERT: A 364 ARG cc_start: 0.6488 (ttm170) cc_final: 0.5801 (OUTLIER) REVERT: A 402 GLU cc_start: 0.7314 (pp20) cc_final: 0.7050 (pp20) REVERT: A 507 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7147 (tpm170) REVERT: A 574 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (tppt) REVERT: A 627 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: A 689 ASP cc_start: 0.7101 (p0) cc_final: 0.6773 (p0) REVERT: A 758 MET cc_start: 0.8671 (mtp) cc_final: 0.8400 (mtm) REVERT: A 797 LEU cc_start: 0.6922 (pt) cc_final: 0.6519 (mt) REVERT: A 804 LEU cc_start: 0.8647 (tp) cc_final: 0.8405 (mt) REVERT: A 897 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7266 (mmt180) REVERT: A 988 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: A 989 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 1023 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.4798 (ttm) REVERT: A 1026 LYS cc_start: 0.5576 (tmmt) cc_final: 0.5264 (mptm) REVERT: B 146 ILE cc_start: 0.8618 (mt) cc_final: 0.8361 (tt) REVERT: B 163 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8259 (ptmt) REVERT: B 294 ASN cc_start: 0.8073 (p0) cc_final: 0.7772 (p0) REVERT: B 402 GLU cc_start: 0.7274 (pp20) cc_final: 0.6997 (pp20) REVERT: B 507 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7146 (tpm170) REVERT: B 627 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: B 689 ASP cc_start: 0.7108 (p0) cc_final: 0.6778 (p0) REVERT: B 758 MET cc_start: 0.8673 (mtp) cc_final: 0.8396 (mtm) REVERT: B 797 LEU cc_start: 0.6933 (pt) cc_final: 0.6517 (mt) REVERT: B 804 LEU cc_start: 0.8653 (tp) cc_final: 0.8412 (mt) REVERT: B 897 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7267 (mmt180) REVERT: B 1023 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.4804 (ttm) REVERT: B 1026 LYS cc_start: 0.5576 (tmmt) cc_final: 0.5265 (mptm) REVERT: C 123 ASP cc_start: 0.6897 (m-30) cc_final: 0.6026 (p0) REVERT: C 146 ILE cc_start: 0.8618 (mt) cc_final: 0.8358 (tt) REVERT: C 163 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8265 (ptmt) REVERT: C 294 ASN cc_start: 0.8099 (p0) cc_final: 0.7788 (p0) REVERT: C 402 GLU cc_start: 0.7276 (pp20) cc_final: 0.6999 (pp20) REVERT: C 507 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7143 (tpm170) REVERT: C 627 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: C 689 ASP cc_start: 0.7105 (p0) cc_final: 0.6781 (p0) REVERT: C 758 MET cc_start: 0.8671 (mtp) cc_final: 0.8395 (mtm) REVERT: C 797 LEU cc_start: 0.6792 (pt) cc_final: 0.6397 (mt) REVERT: C 804 LEU cc_start: 0.8645 (tp) cc_final: 0.8413 (mt) REVERT: C 897 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7265 (mmt180) REVERT: C 1023 MET cc_start: 0.6792 (mmm) cc_final: 0.4846 (ttm) REVERT: C 1026 LYS cc_start: 0.5548 (tmmt) cc_final: 0.5241 (mptm) REVERT: D 123 ASP cc_start: 0.6848 (m-30) cc_final: 0.6026 (p0) REVERT: D 146 ILE cc_start: 0.8621 (mt) cc_final: 0.8361 (tt) REVERT: D 163 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8264 (ptmt) REVERT: D 294 ASN cc_start: 0.8076 (p0) cc_final: 0.7764 (p0) REVERT: D 402 GLU cc_start: 0.7285 (pp20) cc_final: 0.7003 (pp20) REVERT: D 507 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7143 (tpm170) REVERT: D 627 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: D 689 ASP cc_start: 0.7109 (p0) cc_final: 0.6786 (p0) REVERT: D 758 MET cc_start: 0.8669 (mtp) cc_final: 0.8398 (mtm) REVERT: D 797 LEU cc_start: 0.6821 (pt) cc_final: 0.6417 (mt) REVERT: D 804 LEU cc_start: 0.8642 (tp) cc_final: 0.8409 (mt) REVERT: D 897 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7264 (mmt180) REVERT: D 988 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6231 (pm20) REVERT: D 989 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7470 (t0) REVERT: D 1023 MET cc_start: 0.6791 (mmm) cc_final: 0.4849 (ttm) REVERT: D 1026 LYS cc_start: 0.5559 (tmmt) cc_final: 0.5251 (mptm) outliers start: 128 outliers final: 61 residues processed: 446 average time/residue: 1.3932 time to fit residues: 739.4567 Evaluate side-chains 404 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 328 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 359 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31188 Z= 0.211 Angle : 0.590 10.057 42252 Z= 0.299 Chirality : 0.040 0.137 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.121 51.382 4024 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.46 % Allowed : 18.06 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3656 helix: 1.12 (0.11), residues: 2448 sheet: -1.14 (0.35), residues: 200 loop : -2.09 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 786 HIS 0.004 0.001 HIS A 845 PHE 0.012 0.001 PHE B 752 TYR 0.034 0.002 TYR A 191 ARG 0.007 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 349 time to evaluate : 3.262 Fit side-chains REVERT: A 146 ILE cc_start: 0.8623 (mt) cc_final: 0.8270 (tt) REVERT: A 153 LYS cc_start: 0.5578 (pttt) cc_final: 0.5114 (pmtt) REVERT: A 163 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8213 (ptmt) REVERT: A 292 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6647 (p0) REVERT: A 294 ASN cc_start: 0.8048 (p0) cc_final: 0.7742 (p0) REVERT: A 402 GLU cc_start: 0.7337 (pp20) cc_final: 0.7092 (pp20) REVERT: A 627 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 689 ASP cc_start: 0.7007 (p0) cc_final: 0.6741 (p0) REVERT: A 797 LEU cc_start: 0.7148 (pt) cc_final: 0.6738 (mt) REVERT: A 804 LEU cc_start: 0.8605 (tp) cc_final: 0.8383 (mt) REVERT: A 897 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7205 (mmt180) REVERT: A 953 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 988 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6090 (pm20) REVERT: A 989 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 1023 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.4790 (ttm) REVERT: A 1026 LYS cc_start: 0.5564 (tmmt) cc_final: 0.5232 (mptm) REVERT: B 146 ILE cc_start: 0.8620 (mt) cc_final: 0.8264 (tt) REVERT: B 163 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8214 (ptmt) REVERT: B 201 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 294 ASN cc_start: 0.8060 (p0) cc_final: 0.7763 (p0) REVERT: B 402 GLU cc_start: 0.7320 (pp20) cc_final: 0.7084 (pp20) REVERT: B 627 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: B 666 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: B 689 ASP cc_start: 0.7035 (p0) cc_final: 0.6743 (p0) REVERT: B 797 LEU cc_start: 0.7158 (pt) cc_final: 0.6739 (mt) REVERT: B 804 LEU cc_start: 0.8613 (tp) cc_final: 0.8388 (mt) REVERT: B 897 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7207 (mmt180) REVERT: B 944 ASP cc_start: 0.7345 (t0) cc_final: 0.6996 (p0) REVERT: B 953 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7197 (mt-10) REVERT: B 1023 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.4792 (ttm) REVERT: B 1026 LYS cc_start: 0.5509 (tmmt) cc_final: 0.5241 (mptm) REVERT: C 123 ASP cc_start: 0.6936 (m-30) cc_final: 0.5938 (p0) REVERT: C 146 ILE cc_start: 0.8620 (mt) cc_final: 0.8265 (tt) REVERT: C 163 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8219 (ptmt) REVERT: C 201 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 294 ASN cc_start: 0.8084 (p0) cc_final: 0.7782 (p0) REVERT: C 627 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: C 666 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: C 689 ASP cc_start: 0.7036 (p0) cc_final: 0.6746 (p0) REVERT: C 797 LEU cc_start: 0.7148 (pt) cc_final: 0.6725 (mt) REVERT: C 804 LEU cc_start: 0.8612 (tp) cc_final: 0.8396 (mt) REVERT: C 897 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7210 (mmt180) REVERT: C 944 ASP cc_start: 0.7340 (t0) cc_final: 0.7000 (p0) REVERT: C 953 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 1023 MET cc_start: 0.6747 (mmm) cc_final: 0.4806 (ttm) REVERT: C 1026 LYS cc_start: 0.5479 (tmmt) cc_final: 0.5216 (mptm) REVERT: D 123 ASP cc_start: 0.6926 (m-30) cc_final: 0.5954 (p0) REVERT: D 146 ILE cc_start: 0.8622 (mt) cc_final: 0.8268 (tt) REVERT: D 163 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8217 (ptmt) REVERT: D 294 ASN cc_start: 0.8042 (p0) cc_final: 0.7753 (p0) REVERT: D 402 GLU cc_start: 0.7331 (pp20) cc_final: 0.7091 (pp20) REVERT: D 627 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: D 689 ASP cc_start: 0.7017 (p0) cc_final: 0.6753 (p0) REVERT: D 797 LEU cc_start: 0.7156 (pt) cc_final: 0.6743 (mt) REVERT: D 804 LEU cc_start: 0.8611 (tp) cc_final: 0.8390 (mt) REVERT: D 897 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7204 (mmt180) REVERT: D 953 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7190 (mt-10) REVERT: D 988 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: D 989 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7386 (t0) REVERT: D 1023 MET cc_start: 0.6781 (mmm) cc_final: 0.4833 (ttm) REVERT: D 1026 LYS cc_start: 0.5552 (tmmt) cc_final: 0.5222 (mptm) outliers start: 115 outliers final: 71 residues processed: 441 average time/residue: 1.4101 time to fit residues: 739.0508 Evaluate side-chains 418 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 332 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 200 optimal weight: 40.0000 chunk 358 optimal weight: 0.5980 chunk 224 optimal weight: 10.0000 chunk 218 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A 666 GLN B 136 HIS ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN C 136 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 973 ASN D 136 HIS D 635 ASN D 666 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31188 Z= 0.235 Angle : 0.615 12.381 42252 Z= 0.308 Chirality : 0.040 0.142 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.100 51.147 4024 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.82 % Allowed : 18.69 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3656 helix: 1.21 (0.11), residues: 2440 sheet: -1.02 (0.35), residues: 200 loop : -1.96 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 786 HIS 0.003 0.001 HIS D 765 PHE 0.013 0.001 PHE D 752 TYR 0.025 0.002 TYR D 191 ARG 0.007 0.000 ARG C1079 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 340 time to evaluate : 3.533 Fit side-chains REVERT: A 163 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8238 (ptmt) REVERT: A 189 MET cc_start: 0.7016 (mtm) cc_final: 0.6537 (mtm) REVERT: A 294 ASN cc_start: 0.8056 (p0) cc_final: 0.7762 (p0) REVERT: A 627 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: A 666 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: A 689 ASP cc_start: 0.7024 (p0) cc_final: 0.6766 (p0) REVERT: A 797 LEU cc_start: 0.6917 (pt) cc_final: 0.6534 (mt) REVERT: A 804 LEU cc_start: 0.8616 (tp) cc_final: 0.8380 (mt) REVERT: A 897 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7225 (mmt180) REVERT: A 985 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.6980 (mp) REVERT: A 988 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5868 (pm20) REVERT: A 989 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 1023 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.4795 (ttm) REVERT: A 1026 LYS cc_start: 0.5519 (tmmt) cc_final: 0.5214 (mptm) REVERT: A 1046 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5585 (ttm-80) REVERT: A 1048 GLU cc_start: 0.6836 (pm20) cc_final: 0.6409 (mp0) REVERT: B 163 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8236 (ptmt) REVERT: B 294 ASN cc_start: 0.8080 (p0) cc_final: 0.7791 (p0) REVERT: B 627 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: B 689 ASP cc_start: 0.7027 (p0) cc_final: 0.6770 (p0) REVERT: B 797 LEU cc_start: 0.6948 (pt) cc_final: 0.6561 (mt) REVERT: B 804 LEU cc_start: 0.8622 (tp) cc_final: 0.8387 (mt) REVERT: B 897 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7227 (mmt180) REVERT: B 944 ASP cc_start: 0.7354 (t0) cc_final: 0.7023 (p0) REVERT: B 953 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7244 (mt-10) REVERT: B 1023 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.4799 (ttm) REVERT: B 1026 LYS cc_start: 0.5520 (tmmt) cc_final: 0.5216 (mptm) REVERT: B 1046 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5524 (ttm-80) REVERT: B 1048 GLU cc_start: 0.6698 (pm20) cc_final: 0.6294 (mp0) REVERT: C 153 LYS cc_start: 0.5667 (pmtt) cc_final: 0.4983 (pptt) REVERT: C 163 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8240 (ptmt) REVERT: C 294 ASN cc_start: 0.8102 (p0) cc_final: 0.7807 (p0) REVERT: C 627 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: C 689 ASP cc_start: 0.7028 (p0) cc_final: 0.6766 (p0) REVERT: C 797 LEU cc_start: 0.6832 (pt) cc_final: 0.6422 (mt) REVERT: C 804 LEU cc_start: 0.8633 (tp) cc_final: 0.8393 (mt) REVERT: C 897 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7246 (mmt180) REVERT: C 944 ASP cc_start: 0.7309 (t0) cc_final: 0.7001 (p0) REVERT: C 953 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 1023 MET cc_start: 0.6753 (mmm) cc_final: 0.4810 (ttm) REVERT: C 1026 LYS cc_start: 0.5484 (tmmt) cc_final: 0.5220 (mptm) REVERT: C 1046 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5588 (ttm-80) REVERT: C 1048 GLU cc_start: 0.6840 (pm20) cc_final: 0.6412 (mp0) REVERT: D 153 LYS cc_start: 0.5652 (pmtt) cc_final: 0.4967 (pptt) REVERT: D 163 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8259 (ptmt) REVERT: D 294 ASN cc_start: 0.8024 (p0) cc_final: 0.7698 (p0) REVERT: D 627 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: D 666 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: D 689 ASP cc_start: 0.7031 (p0) cc_final: 0.6782 (p0) REVERT: D 797 LEU cc_start: 0.6921 (pt) cc_final: 0.6531 (mt) REVERT: D 804 LEU cc_start: 0.8626 (tp) cc_final: 0.8389 (mt) REVERT: D 897 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7225 (mmt180) REVERT: D 953 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 985 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7029 (mp) REVERT: D 988 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5956 (pm20) REVERT: D 989 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7421 (t0) REVERT: D 1023 MET cc_start: 0.6785 (mmm) cc_final: 0.4836 (ttm) REVERT: D 1026 LYS cc_start: 0.5559 (tmmt) cc_final: 0.5226 (mptm) REVERT: D 1046 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5513 (ttm-80) REVERT: D 1048 GLU cc_start: 0.6718 (pm20) cc_final: 0.6330 (mp0) outliers start: 127 outliers final: 78 residues processed: 447 average time/residue: 1.4140 time to fit residues: 745.5933 Evaluate side-chains 417 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 321 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1046 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1046 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 0.0980 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 281 optimal weight: 8.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN A 666 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN ** D 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31188 Z= 0.158 Angle : 0.584 14.751 42252 Z= 0.289 Chirality : 0.038 0.139 4708 Planarity : 0.003 0.039 5280 Dihedral : 4.788 43.245 4024 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.43 % Allowed : 20.61 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3656 helix: 1.45 (0.11), residues: 2456 sheet: -0.69 (0.37), residues: 200 loop : -2.05 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 786 HIS 0.002 0.001 HIS B 257 PHE 0.028 0.001 PHE D 807 TYR 0.038 0.001 TYR D 191 ARG 0.007 0.000 ARG D1079 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 369 time to evaluate : 3.827 Fit side-chains REVERT: A 163 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8229 (ptmt) REVERT: A 201 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 294 ASN cc_start: 0.7909 (p0) cc_final: 0.7622 (p0) REVERT: A 402 GLU cc_start: 0.7348 (pp20) cc_final: 0.7096 (pp20) REVERT: A 689 ASP cc_start: 0.6884 (p0) cc_final: 0.6645 (p0) REVERT: A 758 MET cc_start: 0.8684 (mtp) cc_final: 0.8479 (mtm) REVERT: A 797 LEU cc_start: 0.7092 (pt) cc_final: 0.6825 (mt) REVERT: A 804 LEU cc_start: 0.8503 (tp) cc_final: 0.8255 (mt) REVERT: A 863 MET cc_start: 0.7940 (mmt) cc_final: 0.7546 (mmt) REVERT: A 897 ARG cc_start: 0.7395 (mtt180) cc_final: 0.7081 (mmt180) REVERT: A 953 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 985 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6899 (mp) REVERT: A 988 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: A 1023 MET cc_start: 0.6398 (mmt) cc_final: 0.4974 (ttp) REVERT: A 1026 LYS cc_start: 0.5567 (tmmt) cc_final: 0.5258 (mptm) REVERT: A 1048 GLU cc_start: 0.6897 (pm20) cc_final: 0.6541 (mp0) REVERT: A 1051 GLU cc_start: 0.7500 (tp30) cc_final: 0.7262 (tp30) REVERT: B 163 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8231 (ptmt) REVERT: B 201 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.7650 (tp) REVERT: B 294 ASN cc_start: 0.8037 (p0) cc_final: 0.7739 (p0) REVERT: B 402 GLU cc_start: 0.7361 (pp20) cc_final: 0.7146 (pp20) REVERT: B 666 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: B 689 ASP cc_start: 0.6886 (p0) cc_final: 0.6645 (p0) REVERT: B 797 LEU cc_start: 0.7065 (pt) cc_final: 0.6802 (mt) REVERT: B 804 LEU cc_start: 0.8507 (tp) cc_final: 0.8261 (mt) REVERT: B 863 MET cc_start: 0.7947 (mmt) cc_final: 0.7549 (mmt) REVERT: B 897 ARG cc_start: 0.7397 (mtt180) cc_final: 0.7078 (mmt180) REVERT: B 953 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7120 (mt-10) REVERT: B 986 VAL cc_start: 0.8090 (m) cc_final: 0.7708 (t) REVERT: B 1023 MET cc_start: 0.6399 (mmt) cc_final: 0.4977 (ttp) REVERT: B 1026 LYS cc_start: 0.5568 (tmmt) cc_final: 0.5262 (mptm) REVERT: B 1046 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5532 (ttm-80) REVERT: B 1048 GLU cc_start: 0.6813 (pm20) cc_final: 0.6469 (mp0) REVERT: B 1051 GLU cc_start: 0.7498 (tp30) cc_final: 0.7267 (tp30) REVERT: C 153 LYS cc_start: 0.5364 (pmtt) cc_final: 0.4747 (pptt) REVERT: C 158 LYS cc_start: 0.6900 (mtmm) cc_final: 0.5905 (pttp) REVERT: C 163 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8209 (ptmt) REVERT: C 201 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7653 (tp) REVERT: C 294 ASN cc_start: 0.8035 (p0) cc_final: 0.7734 (p0) REVERT: C 666 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: C 689 ASP cc_start: 0.6880 (p0) cc_final: 0.6646 (p0) REVERT: C 797 LEU cc_start: 0.7318 (pt) cc_final: 0.7033 (mt) REVERT: C 804 LEU cc_start: 0.8497 (tp) cc_final: 0.8264 (mt) REVERT: C 863 MET cc_start: 0.7949 (mmt) cc_final: 0.7553 (mmt) REVERT: C 897 ARG cc_start: 0.7385 (mtt180) cc_final: 0.7077 (mmt180) REVERT: C 953 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 1023 MET cc_start: 0.6721 (mmm) cc_final: 0.5118 (ttp) REVERT: C 1026 LYS cc_start: 0.5535 (tmmt) cc_final: 0.5262 (mptm) REVERT: C 1048 GLU cc_start: 0.6899 (pm20) cc_final: 0.6541 (mp0) REVERT: C 1051 GLU cc_start: 0.7518 (tp30) cc_final: 0.7277 (tp30) REVERT: D 123 ASP cc_start: 0.6871 (m-30) cc_final: 0.5901 (p0) REVERT: D 153 LYS cc_start: 0.5415 (pmtt) cc_final: 0.4779 (pptt) REVERT: D 158 LYS cc_start: 0.6888 (mtmm) cc_final: 0.5906 (pttp) REVERT: D 163 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8207 (ptmt) REVERT: D 201 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.7656 (tp) REVERT: D 294 ASN cc_start: 0.8014 (p0) cc_final: 0.7698 (p0) REVERT: D 402 GLU cc_start: 0.7362 (pp20) cc_final: 0.7149 (pp20) REVERT: D 689 ASP cc_start: 0.6942 (p0) cc_final: 0.6679 (p0) REVERT: D 758 MET cc_start: 0.8678 (mtp) cc_final: 0.8469 (mtm) REVERT: D 797 LEU cc_start: 0.7292 (pt) cc_final: 0.7034 (mt) REVERT: D 804 LEU cc_start: 0.8500 (tp) cc_final: 0.8264 (mt) REVERT: D 863 MET cc_start: 0.7949 (mmt) cc_final: 0.7559 (mmt) REVERT: D 897 ARG cc_start: 0.7390 (mtt180) cc_final: 0.7074 (mmt180) REVERT: D 953 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7070 (mt-10) REVERT: D 985 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6948 (mp) REVERT: D 988 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6160 (pm20) REVERT: D 1023 MET cc_start: 0.6702 (mmm) cc_final: 0.5131 (ttp) REVERT: D 1026 LYS cc_start: 0.5554 (tmmt) cc_final: 0.5274 (mptm) REVERT: D 1046 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5518 (ttm-80) REVERT: D 1048 GLU cc_start: 0.6807 (pm20) cc_final: 0.6419 (mp0) REVERT: D 1051 GLU cc_start: 0.7522 (tp30) cc_final: 0.7279 (tp30) outliers start: 81 outliers final: 28 residues processed: 429 average time/residue: 1.5119 time to fit residues: 764.1163 Evaluate side-chains 347 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 307 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1046 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 316 optimal weight: 0.9980 chunk 332 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 973 ASN B 666 GLN B 946 HIS B 973 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 946 HIS D 666 GLN D 973 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31188 Z= 0.254 Angle : 0.633 14.626 42252 Z= 0.316 Chirality : 0.041 0.165 4708 Planarity : 0.004 0.043 5280 Dihedral : 4.985 51.331 4024 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.85 % Allowed : 20.91 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3656 helix: 1.34 (0.11), residues: 2444 sheet: -0.49 (0.37), residues: 200 loop : -1.82 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 786 HIS 0.004 0.001 HIS B 765 PHE 0.020 0.001 PHE C 807 TYR 0.025 0.002 TYR A 191 ARG 0.010 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 342 time to evaluate : 3.686 Fit side-chains REVERT: A 158 LYS cc_start: 0.7492 (mppt) cc_final: 0.6119 (pttp) REVERT: A 163 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8200 (ptmt) REVERT: A 294 ASN cc_start: 0.7987 (p0) cc_final: 0.7699 (p0) REVERT: A 666 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: A 689 ASP cc_start: 0.6989 (p0) cc_final: 0.6726 (p0) REVERT: A 797 LEU cc_start: 0.7004 (pt) cc_final: 0.6604 (mt) REVERT: A 804 LEU cc_start: 0.8619 (tp) cc_final: 0.8334 (mt) REVERT: A 897 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7267 (mmt180) REVERT: A 985 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6742 (mp) REVERT: A 988 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: A 1023 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5009 (ttp) REVERT: A 1026 LYS cc_start: 0.5532 (tmmt) cc_final: 0.5219 (mptm) REVERT: A 1046 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5871 (ttm-80) REVERT: A 1048 GLU cc_start: 0.6787 (pm20) cc_final: 0.6540 (mp0) REVERT: B 158 LYS cc_start: 0.7540 (mppt) cc_final: 0.6127 (pttp) REVERT: B 163 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8178 (ptmt) REVERT: B 294 ASN cc_start: 0.8062 (p0) cc_final: 0.7750 (p0) REVERT: B 666 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: B 689 ASP cc_start: 0.6986 (p0) cc_final: 0.6732 (p0) REVERT: B 797 LEU cc_start: 0.6976 (pt) cc_final: 0.6581 (mt) REVERT: B 804 LEU cc_start: 0.8630 (tp) cc_final: 0.8342 (mt) REVERT: B 897 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7269 (mmt180) REVERT: B 953 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 1023 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5016 (ttp) REVERT: B 1026 LYS cc_start: 0.5538 (tmmt) cc_final: 0.5224 (mptm) REVERT: B 1046 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5502 (ttm-80) REVERT: B 1048 GLU cc_start: 0.6881 (pm20) cc_final: 0.6508 (mp0) REVERT: C 123 ASP cc_start: 0.6958 (m-30) cc_final: 0.6001 (p0) REVERT: C 153 LYS cc_start: 0.5533 (pmtt) cc_final: 0.4861 (pptt) REVERT: C 163 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8184 (ptmt) REVERT: C 294 ASN cc_start: 0.8087 (p0) cc_final: 0.7768 (p0) REVERT: C 666 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: C 689 ASP cc_start: 0.6990 (p0) cc_final: 0.6734 (p0) REVERT: C 797 LEU cc_start: 0.7161 (pt) cc_final: 0.6735 (mt) REVERT: C 804 LEU cc_start: 0.8604 (tp) cc_final: 0.8368 (mt) REVERT: C 897 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7270 (mmt180) REVERT: C 1026 LYS cc_start: 0.5468 (tmmt) cc_final: 0.5192 (mptm) REVERT: C 1046 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5872 (ttm-80) REVERT: C 1048 GLU cc_start: 0.6786 (pm20) cc_final: 0.6540 (mp0) REVERT: D 123 ASP cc_start: 0.6949 (m-30) cc_final: 0.6001 (p0) REVERT: D 153 LYS cc_start: 0.5477 (pmtt) cc_final: 0.4815 (pptt) REVERT: D 163 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8202 (ptmt) REVERT: D 294 ASN cc_start: 0.8063 (p0) cc_final: 0.7747 (p0) REVERT: D 666 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: D 689 ASP cc_start: 0.6992 (p0) cc_final: 0.6735 (p0) REVERT: D 797 LEU cc_start: 0.7208 (pt) cc_final: 0.6766 (mt) REVERT: D 804 LEU cc_start: 0.8599 (tp) cc_final: 0.8372 (mt) REVERT: D 897 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7265 (mmt180) REVERT: D 985 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7034 (mp) REVERT: D 988 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: D 1026 LYS cc_start: 0.5483 (tmmt) cc_final: 0.5202 (mptm) REVERT: D 1046 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5493 (ttm-80) REVERT: D 1048 GLU cc_start: 0.6889 (pm20) cc_final: 0.6512 (mp0) outliers start: 95 outliers final: 52 residues processed: 412 average time/residue: 1.4320 time to fit residues: 702.7203 Evaluate side-chains 375 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 309 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 1046 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1046 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 227 optimal weight: 0.1980 chunk 180 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS B 666 GLN B 818 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 818 HIS D 666 GLN D 818 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31188 Z= 0.196 Angle : 0.619 15.280 42252 Z= 0.307 Chirality : 0.040 0.160 4708 Planarity : 0.004 0.044 5280 Dihedral : 4.892 48.796 4024 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.70 % Allowed : 21.57 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3656 helix: 1.37 (0.11), residues: 2448 sheet: -0.76 (0.36), residues: 200 loop : -1.84 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 786 HIS 0.004 0.001 HIS A 667 PHE 0.015 0.001 PHE B 165 TYR 0.020 0.001 TYR B 191 ARG 0.010 0.000 ARG C 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 328 time to evaluate : 3.429 Fit side-chains REVERT: A 158 LYS cc_start: 0.7397 (mppt) cc_final: 0.6085 (pttp) REVERT: A 163 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8278 (ptmt) REVERT: A 294 ASN cc_start: 0.7993 (p0) cc_final: 0.7715 (p0) REVERT: A 689 ASP cc_start: 0.6883 (p0) cc_final: 0.6652 (p0) REVERT: A 797 LEU cc_start: 0.7191 (pt) cc_final: 0.6743 (mt) REVERT: A 804 LEU cc_start: 0.8521 (tp) cc_final: 0.8253 (mt) REVERT: A 897 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7226 (mmt180) REVERT: A 985 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 988 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: A 1023 MET cc_start: 0.6476 (mmt) cc_final: 0.4993 (ttp) REVERT: A 1026 LYS cc_start: 0.5535 (tmmt) cc_final: 0.5219 (mptm) REVERT: A 1048 GLU cc_start: 0.6816 (pm20) cc_final: 0.6577 (mp0) REVERT: A 1051 GLU cc_start: 0.7685 (tp30) cc_final: 0.6896 (tp30) REVERT: A 1079 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6813 (ttm-80) REVERT: B 153 LYS cc_start: 0.5396 (pmtt) cc_final: 0.4680 (pptt) REVERT: B 158 LYS cc_start: 0.7437 (mppt) cc_final: 0.6142 (pttp) REVERT: B 163 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8268 (ptmt) REVERT: B 294 ASN cc_start: 0.8069 (p0) cc_final: 0.7763 (p0) REVERT: B 689 ASP cc_start: 0.6887 (p0) cc_final: 0.6650 (p0) REVERT: B 797 LEU cc_start: 0.7196 (pt) cc_final: 0.6741 (mt) REVERT: B 804 LEU cc_start: 0.8537 (tp) cc_final: 0.8268 (mt) REVERT: B 897 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7231 (mmt180) REVERT: B 953 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 1023 MET cc_start: 0.6482 (mmt) cc_final: 0.4996 (ttp) REVERT: B 1026 LYS cc_start: 0.5536 (tmmt) cc_final: 0.5222 (mptm) REVERT: B 1046 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5514 (ttm-80) REVERT: B 1048 GLU cc_start: 0.6902 (pm20) cc_final: 0.6569 (mp0) REVERT: B 1051 GLU cc_start: 0.7690 (tp30) cc_final: 0.6896 (tp30) REVERT: C 153 LYS cc_start: 0.5476 (pmtt) cc_final: 0.4867 (pptt) REVERT: C 158 LYS cc_start: 0.6810 (mtmm) cc_final: 0.5776 (pttp) REVERT: C 163 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8271 (ptmt) REVERT: C 294 ASN cc_start: 0.8071 (p0) cc_final: 0.7759 (p0) REVERT: C 518 ASP cc_start: 0.7529 (t70) cc_final: 0.7322 (t70) REVERT: C 689 ASP cc_start: 0.6887 (p0) cc_final: 0.6654 (p0) REVERT: C 797 LEU cc_start: 0.7053 (pt) cc_final: 0.6669 (mt) REVERT: C 804 LEU cc_start: 0.8551 (tp) cc_final: 0.8291 (mt) REVERT: C 897 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7214 (mmt180) REVERT: C 953 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7199 (mt-10) REVERT: C 1023 MET cc_start: 0.6542 (mmp) cc_final: 0.5010 (ttm) REVERT: C 1026 LYS cc_start: 0.5447 (tmmt) cc_final: 0.5203 (mptm) REVERT: C 1048 GLU cc_start: 0.6818 (pm20) cc_final: 0.6576 (mp0) REVERT: C 1051 GLU cc_start: 0.7690 (tp30) cc_final: 0.6896 (tp30) REVERT: C 1079 ARG cc_start: 0.7259 (ttp80) cc_final: 0.6834 (ttm-80) REVERT: D 153 LYS cc_start: 0.5408 (pmtt) cc_final: 0.4806 (pptt) REVERT: D 158 LYS cc_start: 0.6784 (mtmm) cc_final: 0.5764 (pttp) REVERT: D 163 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8265 (ptmt) REVERT: D 294 ASN cc_start: 0.8044 (p0) cc_final: 0.7734 (p0) REVERT: D 689 ASP cc_start: 0.6909 (p0) cc_final: 0.6681 (p0) REVERT: D 797 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6833 (mt) REVERT: D 804 LEU cc_start: 0.8551 (tp) cc_final: 0.8305 (mt) REVERT: D 897 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7210 (mmt180) REVERT: D 953 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7187 (mt-10) REVERT: D 985 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6877 (mp) REVERT: D 988 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6234 (pm20) REVERT: D 1023 MET cc_start: 0.6485 (mmp) cc_final: 0.4942 (ttm) REVERT: D 1026 LYS cc_start: 0.5460 (tmmt) cc_final: 0.5214 (mptm) REVERT: D 1046 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5506 (ttm-80) REVERT: D 1048 GLU cc_start: 0.6907 (pm20) cc_final: 0.6571 (mp0) REVERT: D 1051 GLU cc_start: 0.7683 (tp30) cc_final: 0.6889 (tp30) REVERT: D 1078 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4982 (mtt) REVERT: D 1079 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6862 (ttm-80) outliers start: 90 outliers final: 52 residues processed: 399 average time/residue: 1.3868 time to fit residues: 655.2760 Evaluate side-chains 369 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 309 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 792 ASN Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1046 ARG Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 5.9990 chunk 314 optimal weight: 0.1980 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.170409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124626 restraints weight = 47187.106| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.36 r_work: 0.3403 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31188 Z= 0.192 Angle : 0.610 15.145 42252 Z= 0.303 Chirality : 0.039 0.164 4708 Planarity : 0.004 0.046 5280 Dihedral : 4.806 48.027 4024 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.37 % Allowed : 22.21 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3656 helix: 1.38 (0.11), residues: 2452 sheet: -0.72 (0.36), residues: 200 loop : -1.74 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 786 HIS 0.002 0.001 HIS D 845 PHE 0.026 0.001 PHE C 807 TYR 0.022 0.001 TYR C 191 ARG 0.010 0.000 ARG B1079 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12675.69 seconds wall clock time: 248 minutes 54.94 seconds (14934.94 seconds total)