Starting phenix.real_space_refine on Mon Feb 19 10:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/02_2024/7zh2_14718_updated.pdb" } resolution = 2.71 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15597 2.51 5 N 3986 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 755": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24419 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7959 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.97, per 1000 atoms: 0.57 Number of scatterers: 24419 At special positions: 0 Unit cell: (131.25, 143.85, 158.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4704 8.00 N 3986 7.00 C 15597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 318 " " NAG A1307 " - " ASN A 357 " " NAG A1308 " - " ASN A 602 " " NAG A1309 " - " ASN A 783 " " NAG A1310 " - " ASN A 699 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 357 " " NAG B1308 " - " ASN B 602 " " NAG B1309 " - " ASN B 783 " " NAG B1310 " - " ASN B 699 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 158 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1309 " - " ASN C 783 " " NAG C1310 " - " ASN C 699 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 9.28 Conformation dependent library (CDL) restraints added in 4.2 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 39 sheets defined 22.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.917A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.365A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 720 through 723 No H-bonds generated for 'chain 'A' and resid 720 through 723' Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 742 through 764 removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.553A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 864 Processing helix chain 'A' and resid 883 through 891 Processing helix chain 'A' and resid 896 through 921 removed outlier: 5.794A pdb=" N LYS A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.555A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 removed outlier: 3.704A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.544A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.864A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 removed outlier: 4.209A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 720 through 723 No H-bonds generated for 'chain 'B' and resid 720 through 723' Processing helix chain 'B' and resid 729 through 738 Processing helix chain 'B' and resid 742 through 764 removed outlier: 3.737A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 819 through 825 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 864 Processing helix chain 'B' and resid 882 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 902 through 921 Processing helix chain 'B' and resid 925 through 949 removed outlier: 4.578A pdb=" N LYS B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 936 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 945 " --> pdb=" O ASN B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 removed outlier: 3.679A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.587A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 391 through 396 removed outlier: 4.507A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 426 through 429 No H-bonds generated for 'chain 'C' and resid 426 through 429' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 720 through 723 No H-bonds generated for 'chain 'C' and resid 720 through 723' Processing helix chain 'C' and resid 729 through 738 Processing helix chain 'C' and resid 742 through 764 removed outlier: 3.670A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 removed outlier: 3.528A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 863 Processing helix chain 'C' and resid 882 through 891 removed outlier: 3.506A pdb=" N GLY C 890 " --> pdb=" O TYR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.582A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 921 removed outlier: 3.628A pdb=" N SER C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 949 removed outlier: 4.213A pdb=" N LYS C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 948 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 949 " --> pdb=" O LYS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 removed outlier: 3.584A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.823A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.674A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.014A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 127 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= E, first strand: chain 'A' and resid 312 through 315 removed outlier: 8.421A pdb=" N VAL A 313 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 526 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG A 315 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN A 528 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.649A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 348 through 350 Processing sheet with id= H, first strand: chain 'A' and resid 439 through 441 Processing sheet with id= I, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.391A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.976A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.578A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.693A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.665A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.080A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.649A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.791A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 636 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 312 through 315 removed outlier: 8.388A pdb=" N VAL B 313 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN B 526 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG B 315 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN B 528 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.686A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= T, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= U, first strand: chain 'B' and resid 674 through 678 removed outlier: 6.440A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 693 through 697 Processing sheet with id= W, first strand: chain 'B' and resid 699 through 710 removed outlier: 3.553A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.590A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id= Z, first strand: chain 'C' and resid 31 through 35 removed outlier: 3.925A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.129A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 161 through 164 removed outlier: 4.424A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.591A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 312 through 315 removed outlier: 8.530A pdb=" N VAL C 313 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN C 526 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ARG C 315 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN C 528 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.664A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= AG, first strand: chain 'C' and resid 439 through 441 Processing sheet with id= AH, first strand: chain 'C' and resid 674 through 678 removed outlier: 6.475A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 693 through 697 Processing sheet with id= AJ, first strand: chain 'C' and resid 699 through 710 removed outlier: 3.645A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.565A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 4.147A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1076 through 1079 879 hydrogen bonds defined for protein. 2352 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: 8.99 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6006 1.33 - 1.46: 6550 1.46 - 1.58: 12235 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 24971 Sorted by residual: bond pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.42e+01 bond pdb=" N ILE C 787 " pdb=" CA ILE C 787 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.36e+01 bond pdb=" N ILE C 81 " pdb=" CA ILE C 81 " ideal model delta sigma weight residual 1.460 1.494 -0.034 9.30e-03 1.16e+04 1.32e+01 bond pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" N CYS A 159 " pdb=" CA CYS A 159 " ideal model delta sigma weight residual 1.454 1.497 -0.042 1.31e-02 5.83e+03 1.05e+01 ... (remaining 24966 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 693 106.85 - 113.63: 13653 113.63 - 120.41: 9006 120.41 - 127.19: 10375 127.19 - 133.97: 206 Bond angle restraints: 33933 Sorted by residual: angle pdb=" C PHE A 880 " pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA PHE A 880 " pdb=" C PHE A 880 " pdb=" O PHE A 880 " ideal model delta sigma weight residual 121.16 114.28 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" C SER C 785 " pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 121.54 133.21 -11.67 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C ASN A 158 " pdb=" CA ASN A 158 " pdb=" CB ASN A 158 " ideal model delta sigma weight residual 111.86 119.38 -7.52 1.34e+00 5.57e-01 3.15e+01 angle pdb=" CA SER C 785 " pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 121.16 114.88 6.28 1.12e+00 7.97e-01 3.14e+01 ... (remaining 33928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14033 17.96 - 35.91: 1002 35.91 - 53.87: 179 53.87 - 71.83: 52 71.83 - 89.78: 23 Dihedral angle restraints: 15289 sinusoidal: 6358 harmonic: 8931 Sorted by residual: dihedral pdb=" CA THR C 468 " pdb=" C THR C 468 " pdb=" N PRO C 469 " pdb=" CA PRO C 469 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 468 " pdb=" C THR B 468 " pdb=" N PRO B 469 " pdb=" CA PRO B 469 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -53.86 -32.14 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 15286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3151 0.048 - 0.096: 485 0.096 - 0.145: 265 0.145 - 0.193: 9 0.193 - 0.241: 7 Chirality restraints: 3917 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.55e+00 chirality pdb=" CA ILE A 878 " pdb=" N ILE A 878 " pdb=" C ILE A 878 " pdb=" CB ILE A 878 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.43e+00 ... (remaining 3914 not shown) Planarity restraints: 4382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 158 " 0.049 2.00e-02 2.50e+03 4.71e-02 2.78e+01 pdb=" CG ASN A 158 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 158 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 158 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 158 " -0.043 2.00e-02 2.50e+03 4.57e-02 2.61e+01 pdb=" CG ASN C 158 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 158 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 158 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1093 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A1094 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A1094 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1094 " 0.057 5.00e-02 4.00e+02 ... (remaining 4379 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 130 2.61 - 3.18: 20371 3.18 - 3.76: 33944 3.76 - 4.33: 51056 4.33 - 4.90: 84462 Nonbonded interactions: 189963 Sorted by model distance: nonbonded pdb=" O ASN C 119 " pdb=" OG SER C 120 " model vdw 2.038 2.440 nonbonded pdb=" O ASN A 119 " pdb=" OG SER A 120 " model vdw 2.042 2.440 nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASN B 108 " model vdw 2.216 2.440 nonbonded pdb=" O PRO B 462 " pdb=" NZ LYS B 465 " model vdw 2.271 2.520 nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.278 2.440 ... (remaining 189958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1105 or resid 1301 through 1310)) selection = (chain 'B' and (resid 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1105 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.680 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: 0.030 Extract box with map and model: 4.560 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 65.290 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24971 Z= 0.224 Angle : 0.622 12.049 33933 Z= 0.361 Chirality : 0.045 0.241 3917 Planarity : 0.004 0.106 4352 Dihedral : 13.216 89.781 9433 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3018 helix: 0.51 (0.20), residues: 684 sheet: 0.70 (0.20), residues: 627 loop : -1.53 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 423 HIS 0.007 0.001 HIS A1065 PHE 0.027 0.001 PHE A 334 TYR 0.009 0.001 TYR C 491 ARG 0.010 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 343 time to evaluate : 2.664 Fit side-chains revert: symmetry clash REVERT: A 713 MET cc_start: 0.8644 (ptm) cc_final: 0.8203 (ptm) REVERT: A 1058 THR cc_start: 0.7318 (m) cc_final: 0.6923 (p) REVERT: A 1103 PHE cc_start: 0.6377 (p90) cc_final: 0.5884 (p90) REVERT: B 484 TYR cc_start: 0.7637 (m-80) cc_final: 0.7388 (m-80) REVERT: B 758 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7195 (ttp80) REVERT: B 790 ASP cc_start: 0.6752 (t0) cc_final: 0.6065 (t70) REVERT: B 884 MET cc_start: 0.7678 (tpt) cc_final: 0.7226 (tpt) REVERT: B 1079 PHE cc_start: 0.6356 (t80) cc_final: 0.5602 (t80) REVERT: C 32 GLN cc_start: 0.7308 (mm110) cc_final: 0.7094 (mm110) outliers start: 8 outliers final: 4 residues processed: 346 average time/residue: 1.4812 time to fit residues: 583.6753 Evaluate side-chains 257 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 917 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 692 ASN A 766 GLN A 877 GLN A 889 ASN A 908 GLN A 936 GLN A1088 GLN B 70 HIS B 321 ASN B 479 ASN B 827 ASN B 883 GLN B 889 ASN B 992 GLN C 546 GLN C 769 GLN C 883 GLN ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24971 Z= 0.256 Angle : 0.625 7.789 33933 Z= 0.342 Chirality : 0.048 0.211 3917 Planarity : 0.005 0.068 4352 Dihedral : 7.393 78.285 4034 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 2.20 % Allowed : 5.98 % Favored : 91.82 % 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: -0.55 (0.14), residues: 3018 helix: 1.03 (0.19), residues: 705 sheet: 0.93 (0.22), residues: 555 loop : -1.47 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.008 0.002 HIS C1065 PHE 0.035 0.002 PHE A 334 TYR 0.021 0.002 TYR B 352 ARG 0.006 0.001 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 3.050 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7007 (pp20) cc_final: 0.6752 (pp20) REVERT: A 319 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 449 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7766 (mtt90) REVERT: A 544 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6622 (mtp85) REVERT: A 713 MET cc_start: 0.8610 (ptm) cc_final: 0.8159 (ptm) REVERT: A 730 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: A 1053 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.5931 (mt0) REVERT: A 1054 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: B 306 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6929 (mtt90) REVERT: B 484 TYR cc_start: 0.7754 (m-80) cc_final: 0.7496 (m-80) REVERT: B 758 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7376 (ttp80) REVERT: B 762 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: B 790 ASP cc_start: 0.6839 (t0) cc_final: 0.6259 (t70) REVERT: B 884 MET cc_start: 0.7762 (tpt) cc_final: 0.7382 (tpt) REVERT: C 32 GLN cc_start: 0.7282 (mm110) cc_final: 0.7057 (mm110) REVERT: C 54 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8192 (tp) REVERT: C 449 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: C 809 THR cc_start: 0.7413 (m) cc_final: 0.7003 (p) REVERT: C 887 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7964 (mpt-90) REVERT: C 911 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7285 (tmtt) REVERT: C 1011 MET cc_start: 0.8717 (tpp) cc_final: 0.8507 (tpp) outliers start: 58 outliers final: 26 residues processed: 294 average time/residue: 1.5445 time to fit residues: 516.1978 Evaluate side-chains 282 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1080 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 278 optimal weight: 0.0270 chunk 300 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 276 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 223 optimal weight: 0.0770 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1088 GLN B 70 HIS B 744 GLN B 769 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 96 ASN C 479 ASN C 546 GLN C 737 GLN C 769 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 ASN C 904 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24971 Z= 0.129 Angle : 0.497 14.887 33933 Z= 0.267 Chirality : 0.043 0.227 3917 Planarity : 0.004 0.053 4352 Dihedral : 6.432 70.597 4029 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 1.36 % Allowed : 7.69 % Favored : 90.95 % 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: -0.26 (0.14), residues: 3018 helix: 1.47 (0.20), residues: 699 sheet: 0.88 (0.21), residues: 555 loop : -1.28 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 423 HIS 0.006 0.001 HIS A1065 PHE 0.021 0.001 PHE A 179 TYR 0.017 0.001 TYR C 352 ARG 0.004 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 265 time to evaluate : 2.884 Fit side-chains revert: symmetry clash REVERT: A 544 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6553 (mtp85) REVERT: A 713 MET cc_start: 0.8550 (ptm) cc_final: 0.8177 (ptm) REVERT: A 911 LYS cc_start: 0.7542 (ttpp) cc_final: 0.7177 (mmtm) REVERT: A 1103 PHE cc_start: 0.6183 (p90) cc_final: 0.5623 (p90) REVERT: B 137 PHE cc_start: 0.7233 (p90) cc_final: 0.7020 (p90) REVERT: B 758 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7210 (ttp-110) REVERT: B 762 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: B 790 ASP cc_start: 0.6712 (t0) cc_final: 0.6162 (t70) REVERT: B 799 PHE cc_start: 0.7012 (t80) cc_final: 0.6809 (t80) REVERT: B 884 MET cc_start: 0.7730 (tpt) cc_final: 0.7302 (tpt) REVERT: C 32 GLN cc_start: 0.7239 (mm110) cc_final: 0.7011 (mm110) REVERT: C 54 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8196 (tp) REVERT: C 107 MET cc_start: 0.8099 (mmm) cc_final: 0.7630 (mmt) REVERT: C 449 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7106 (mtp180) REVERT: C 624 THR cc_start: 0.5412 (OUTLIER) cc_final: 0.5029 (t) REVERT: C 632 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6824 (mm-40) REVERT: C 809 THR cc_start: 0.7219 (m) cc_final: 0.6798 (p) REVERT: C 882 MET cc_start: 0.7342 (mtp) cc_final: 0.7108 (mtm) REVERT: C 887 ARG cc_start: 0.8213 (mmt180) cc_final: 0.7974 (mpt-90) outliers start: 36 outliers final: 16 residues processed: 290 average time/residue: 1.5405 time to fit residues: 509.5515 Evaluate side-chains 264 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 6.9990 chunk 209 optimal weight: 0.0770 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 0.0070 chunk 186 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1088 GLN B 178 ASN B 445 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 546 GLN C 769 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24971 Z= 0.273 Angle : 0.632 12.859 33933 Z= 0.344 Chirality : 0.048 0.311 3917 Planarity : 0.005 0.047 4352 Dihedral : 6.912 64.977 4029 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 2.23 % Allowed : 8.94 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 3018 helix: 0.95 (0.19), residues: 729 sheet: 0.85 (0.21), residues: 570 loop : -1.49 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 423 HIS 0.009 0.002 HIS C1065 PHE 0.027 0.002 PHE A 334 TYR 0.022 0.002 TYR B 352 ARG 0.005 0.001 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 256 time to evaluate : 2.813 Fit side-chains revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7685 (mtt90) REVERT: A 544 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6686 (mtp85) REVERT: A 713 MET cc_start: 0.8584 (ptm) cc_final: 0.8289 (ptm) REVERT: A 730 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: A 827 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.5832 (p0) REVERT: A 911 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7209 (mmtm) REVERT: A 1053 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: A 1054 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: A 1088 GLN cc_start: 0.6924 (pt0) cc_final: 0.6683 (pt0) REVERT: B 178 ASN cc_start: 0.4211 (OUTLIER) cc_final: 0.3477 (m-40) REVERT: B 758 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7364 (ttp80) REVERT: B 762 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: B 790 ASP cc_start: 0.6711 (t0) cc_final: 0.6196 (t70) REVERT: B 1098 THR cc_start: 0.5778 (m) cc_final: 0.5404 (p) REVERT: B 1103 PHE cc_start: 0.7539 (p90) cc_final: 0.7250 (p90) REVERT: C 54 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 449 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7138 (mtp180) REVERT: C 624 THR cc_start: 0.6195 (OUTLIER) cc_final: 0.5877 (t) REVERT: C 632 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6947 (mm-40) REVERT: C 809 THR cc_start: 0.7481 (m) cc_final: 0.7109 (p) REVERT: C 887 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7918 (mpt-90) REVERT: C 911 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7248 (tmtt) outliers start: 59 outliers final: 26 residues processed: 294 average time/residue: 1.5736 time to fit residues: 525.3732 Evaluate side-chains 283 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 911 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 201 GLN C 546 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24971 Z= 0.232 Angle : 0.600 11.062 33933 Z= 0.326 Chirality : 0.047 0.268 3917 Planarity : 0.005 0.044 4352 Dihedral : 6.783 56.359 4029 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.50 % Allowed : 9.09 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.14), residues: 3018 helix: 0.91 (0.19), residues: 729 sheet: 0.81 (0.21), residues: 570 loop : -1.54 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.007 0.002 HIS C1065 PHE 0.018 0.002 PHE A 334 TYR 0.020 0.002 TYR B 352 ARG 0.004 0.001 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 251 time to evaluate : 2.564 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8099 (t0) cc_final: 0.7867 (t0) REVERT: A 449 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7694 (mtt90) REVERT: A 544 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6665 (mtp85) REVERT: A 589 ASN cc_start: 0.6382 (OUTLIER) cc_final: 0.5869 (p0) REVERT: A 593 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6612 (tt0) REVERT: A 713 MET cc_start: 0.8445 (ptm) cc_final: 0.8103 (ptm) REVERT: A 730 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: A 827 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5806 (p0) REVERT: A 1053 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6401 (mt0) REVERT: A 1054 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: B 758 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7396 (ttp80) REVERT: B 762 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: B 1098 THR cc_start: 0.5841 (m) cc_final: 0.5496 (p) REVERT: C 54 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 449 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7129 (mtp180) REVERT: C 624 THR cc_start: 0.5728 (OUTLIER) cc_final: 0.5374 (t) REVERT: C 632 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6927 (mm-40) REVERT: C 809 THR cc_start: 0.7462 (m) cc_final: 0.7131 (p) REVERT: C 882 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7330 (mtm) REVERT: C 911 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7240 (tmtt) REVERT: C 917 GLN cc_start: 0.7347 (tt0) cc_final: 0.6914 (tt0) outliers start: 66 outliers final: 30 residues processed: 296 average time/residue: 1.5941 time to fit residues: 539.1112 Evaluate side-chains 282 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 245 optimal weight: 0.3980 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 155 optimal weight: 0.0070 overall best weight: 2.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 74 HIS C 112 GLN C 546 GLN C 769 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS C1095 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24971 Z= 0.194 Angle : 0.561 8.856 33933 Z= 0.305 Chirality : 0.045 0.235 3917 Planarity : 0.004 0.042 4352 Dihedral : 6.479 58.562 4029 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.77 % Allowed : 9.47 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3018 helix: 0.99 (0.19), residues: 729 sheet: 0.74 (0.21), residues: 552 loop : -1.48 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.014 0.002 PHE B 578 TYR 0.019 0.002 TYR B 352 ARG 0.003 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 255 time to evaluate : 2.897 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6818 (mmm) REVERT: A 132 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6654 (mm) REVERT: A 433 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6378 (t) REVERT: A 449 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: A 544 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6658 (mtp85) REVERT: A 589 ASN cc_start: 0.6370 (OUTLIER) cc_final: 0.5883 (p0) REVERT: A 593 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: A 713 MET cc_start: 0.8368 (ptm) cc_final: 0.8080 (ptm) REVERT: A 730 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 827 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5808 (p0) REVERT: A 911 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7199 (mmtm) REVERT: A 1053 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6434 (mt0) REVERT: A 1054 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: B 178 ASN cc_start: 0.4150 (OUTLIER) cc_final: 0.3235 (m-40) REVERT: B 183 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7348 (mtt-85) REVERT: B 758 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7225 (ttp-110) REVERT: B 762 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: B 790 ASP cc_start: 0.6795 (t0) cc_final: 0.6152 (t70) REVERT: B 1098 THR cc_start: 0.5737 (m) cc_final: 0.5417 (p) REVERT: C 54 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8159 (tp) REVERT: C 107 MET cc_start: 0.8095 (mmm) cc_final: 0.7855 (mmt) REVERT: C 449 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7132 (mtp180) REVERT: C 624 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5442 (t) REVERT: C 809 THR cc_start: 0.7466 (m) cc_final: 0.7159 (p) REVERT: C 882 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: C 887 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6578 (mpt-90) REVERT: C 911 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7245 (tmtt) REVERT: C 917 GLN cc_start: 0.7337 (tt0) cc_final: 0.6888 (tt0) outliers start: 73 outliers final: 32 residues processed: 302 average time/residue: 1.5072 time to fit residues: 519.4469 Evaluate side-chains 297 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 887 ARG Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1065 HIS B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 546 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24971 Z= 0.315 Angle : 0.682 9.922 33933 Z= 0.371 Chirality : 0.050 0.269 3917 Planarity : 0.005 0.045 4352 Dihedral : 6.938 59.774 4029 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 3.03 % Allowed : 10.00 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.14), residues: 3018 helix: 0.68 (0.19), residues: 729 sheet: 0.80 (0.21), residues: 564 loop : -1.66 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 423 HIS 0.009 0.002 HIS C1065 PHE 0.019 0.002 PHE B 578 TYR 0.022 0.002 TYR B 352 ARG 0.006 0.001 ARG B 982 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 249 time to evaluate : 2.773 Fit side-chains REVERT: A 72 ILE cc_start: 0.2730 (OUTLIER) cc_final: 0.1803 (tt) REVERT: A 132 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6700 (mm) REVERT: A 268 GLU cc_start: 0.6998 (pp20) cc_final: 0.6776 (pp20) REVERT: A 433 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6413 (t) REVERT: A 544 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6673 (mtp85) REVERT: A 589 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.5888 (p0) REVERT: A 593 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: A 827 ASN cc_start: 0.6207 (OUTLIER) cc_final: 0.5766 (p0) REVERT: A 1053 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6466 (mt0) REVERT: A 1054 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: B 758 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7356 (ttp80) REVERT: B 762 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 790 ASP cc_start: 0.6894 (t0) cc_final: 0.6246 (t70) REVERT: B 1098 THR cc_start: 0.5903 (m) cc_final: 0.5579 (p) REVERT: C 54 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8158 (tp) REVERT: C 107 MET cc_start: 0.8114 (mmm) cc_final: 0.7639 (mmt) REVERT: C 449 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7170 (mtp180) REVERT: C 624 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5648 (t) REVERT: C 882 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7697 (mtm) REVERT: C 911 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7304 (tmtt) outliers start: 80 outliers final: 38 residues processed: 302 average time/residue: 1.4531 time to fit residues: 501.5877 Evaluate side-chains 290 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 145 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 627 ASN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24971 Z= 0.162 Angle : 0.538 9.595 33933 Z= 0.292 Chirality : 0.045 0.215 3917 Planarity : 0.004 0.042 4352 Dihedral : 6.209 55.678 4027 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 1.97 % Allowed : 11.59 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.14), residues: 3018 helix: 0.98 (0.19), residues: 729 sheet: 0.76 (0.21), residues: 552 loop : -1.50 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.013 0.001 PHE B 578 TYR 0.019 0.001 TYR B 352 ARG 0.002 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 252 time to evaluate : 2.546 Fit side-chains REVERT: A 92 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7339 (p) REVERT: A 132 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6687 (mm) REVERT: A 544 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6644 (mtp85) REVERT: A 593 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: A 730 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: A 827 ASN cc_start: 0.6213 (OUTLIER) cc_final: 0.5771 (p0) REVERT: A 1054 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: B 758 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7265 (ttp-110) REVERT: B 762 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: B 1098 THR cc_start: 0.5621 (m) cc_final: 0.5349 (p) REVERT: C 54 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8156 (tp) REVERT: C 107 MET cc_start: 0.8023 (mmm) cc_final: 0.7658 (mmt) REVERT: C 449 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7158 (mtp180) REVERT: C 624 THR cc_start: 0.5599 (OUTLIER) cc_final: 0.5235 (t) REVERT: C 647 GLU cc_start: 0.6202 (tp30) cc_final: 0.5851 (tm-30) REVERT: C 882 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: C 911 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7237 (tmtt) REVERT: C 917 GLN cc_start: 0.7296 (tt0) cc_final: 0.6891 (tt0) outliers start: 52 outliers final: 25 residues processed: 292 average time/residue: 1.5268 time to fit residues: 508.5524 Evaluate side-chains 278 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 0.4980 chunk 273 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1040 HIS B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 ASN B 992 GLN C 32 GLN C 96 ASN C 546 GLN C 769 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24971 Z= 0.173 Angle : 0.541 10.135 33933 Z= 0.293 Chirality : 0.045 0.207 3917 Planarity : 0.004 0.042 4352 Dihedral : 6.055 56.972 4027 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.12 % Allowed : 11.70 % Favored : 86.17 % 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: 3018 helix: 1.05 (0.20), residues: 729 sheet: 0.77 (0.21), residues: 549 loop : -1.48 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.014 0.001 PHE B 799 TYR 0.019 0.001 TYR A 352 ARG 0.002 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 246 time to evaluate : 2.736 Fit side-chains REVERT: A 37 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6587 (mmm) REVERT: A 92 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 132 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6707 (mm) REVERT: A 544 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6648 (mtp85) REVERT: A 593 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: A 730 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6805 (pm20) REVERT: A 827 ASN cc_start: 0.6235 (OUTLIER) cc_final: 0.5780 (p0) REVERT: A 911 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7173 (mmtm) REVERT: A 1054 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6460 (pm20) REVERT: B 758 ARG cc_start: 0.7702 (ttm170) cc_final: 0.7240 (ttp-110) REVERT: B 762 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 1098 THR cc_start: 0.5693 (m) cc_final: 0.5432 (p) REVERT: C 54 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 107 MET cc_start: 0.8068 (mmm) cc_final: 0.7722 (mmt) REVERT: C 449 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7169 (mtp180) REVERT: C 624 THR cc_start: 0.5701 (OUTLIER) cc_final: 0.5341 (t) REVERT: C 647 GLU cc_start: 0.6361 (tp30) cc_final: 0.5965 (tm-30) REVERT: C 882 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: C 911 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7245 (tmtt) REVERT: C 917 GLN cc_start: 0.7293 (tt0) cc_final: 0.6863 (tt0) outliers start: 56 outliers final: 31 residues processed: 286 average time/residue: 1.4968 time to fit residues: 490.1742 Evaluate side-chains 284 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1086 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1040 HIS B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 546 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24971 Z= 0.275 Angle : 0.627 8.746 33933 Z= 0.341 Chirality : 0.048 0.219 3917 Planarity : 0.005 0.042 4352 Dihedral : 6.411 55.764 4026 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.16 % Allowed : 11.78 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3018 helix: 0.82 (0.19), residues: 729 sheet: 0.68 (0.21), residues: 552 loop : -1.54 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 423 HIS 0.008 0.002 HIS C1065 PHE 0.018 0.002 PHE B 799 TYR 0.022 0.002 TYR B 352 ARG 0.005 0.001 ARG C 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 240 time to evaluate : 2.760 Fit side-chains REVERT: A 37 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6630 (mmm) REVERT: A 132 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6718 (mm) REVERT: A 544 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6662 (mtp85) REVERT: A 593 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: A 827 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.5791 (p0) REVERT: A 1054 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: B 758 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7190 (ttp-110) REVERT: B 762 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: B 1098 THR cc_start: 0.5799 (m) cc_final: 0.5525 (p) REVERT: C 54 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8157 (tp) REVERT: C 107 MET cc_start: 0.8113 (mmm) cc_final: 0.7667 (mmt) REVERT: C 306 ARG cc_start: 0.7097 (mmt180) cc_final: 0.6883 (mmt180) REVERT: C 449 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7169 (mtp180) REVERT: C 624 THR cc_start: 0.5956 (OUTLIER) cc_final: 0.5520 (t) REVERT: C 647 GLU cc_start: 0.6317 (tp30) cc_final: 0.5911 (tm-30) REVERT: C 882 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: C 911 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7275 (tmtt) REVERT: C 917 GLN cc_start: 0.7370 (tt0) cc_final: 0.6947 (tt0) outliers start: 57 outliers final: 36 residues processed: 280 average time/residue: 1.5027 time to fit residues: 480.0026 Evaluate side-chains 284 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1086 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 223 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1040 HIS B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 445 HIS C 546 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103736 restraints weight = 28312.169| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.67 r_work: 0.2919 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24971 Z= 0.179 Angle : 0.548 9.600 33933 Z= 0.297 Chirality : 0.045 0.211 3917 Planarity : 0.004 0.042 4352 Dihedral : 6.111 56.881 4026 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.23 % Allowed : 11.59 % Favored : 86.17 % 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: -0.63 (0.14), residues: 3018 helix: 0.97 (0.19), residues: 729 sheet: 0.76 (0.21), residues: 549 loop : -1.51 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.019 0.001 PHE B 799 TYR 0.020 0.001 TYR A 352 ARG 0.002 0.000 ARG C 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8471.04 seconds wall clock time: 151 minutes 34.04 seconds (9094.04 seconds total)