Starting phenix.real_space_refine on Mon Feb 19 03:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h11_34421/02_2024/8h11_34421.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 125 5.16 5 C 15022 2.51 5 N 3863 2.21 5 O 4556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 684": "OD1" <-> "OD2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 727": "OD1" <-> "OD2" Residue "B PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 23566 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7751 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 44, 'TRANS': 947} Chain breaks: 9 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7657 Classifications: {'peptide': 979} Link IDs: {'PTRANS': 46, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7612 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 44, 'TRANS': 929} Chain breaks: 9 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: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 12.19, per 1000 atoms: 0.52 Number of scatterers: 23566 At special positions: 0 Unit cell: (129.21, 133.59, 163.155, 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 125 16.00 O 4556 8.00 N 3863 7.00 C 15022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " 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=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 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 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=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 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 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 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 227 " " NAG A1306 " - " ASN A 269 " " NAG A1307 " - " ASN A 318 " " NAG A1308 " - " ASN A 602 " " NAG A1309 " - " ASN A 691 " " NAG A1310 " - " ASN A 699 " " NAG A1311 " - " ASN A 783 " " NAG A1312 " - " ASN A1056 " " NAG A1313 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 602 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 699 " " NAG B1310 " - " ASN B 783 " " NAG B1311 " - " ASN B1056 " " NAG B1312 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 227 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 602 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C 783 " " NAG C1311 " - " ASN C1056 " " NAG C1312 " - " ASN C1116 " " NAG D 1 " - " ASN B 227 " Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 4.2 seconds 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5526 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 26.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.923A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.802A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 788 removed outlier: 3.622A pdb=" N LEU B 788 " --> pdb=" O SER B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.611A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.526A pdb=" N GLY B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.629A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 894 through 900 removed outlier: 4.138A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 920 removed outlier: 3.548A pdb=" N GLN B 917 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.787A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.685A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.745A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.881A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.126A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.537A pdb=" N ILE A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.626A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 741 through 765 removed outlier: 3.796A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.624A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.715A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.051A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.716A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.618A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.690A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.758A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 4.174A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.763A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 4.021A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.067A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 397 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.503A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.622A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.823A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.684A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 848 through 867 Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 894 through 900 removed outlier: 4.131A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.017A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.641A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.614A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.814A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.509A pdb=" N ARG A 553 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.667A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.678A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 298 through 306 removed outlier: 7.033A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.488A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.090A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 386 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.422A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.053A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 683 through 685 removed outlier: 7.132A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.431A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.431A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.482A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.855A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AC2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.812A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.821A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.917A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.936A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.294A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AC8, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.216A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.550A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.550A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.656A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 769 through 771 removed outlier: 3.534A pdb=" N SER C 685 " --> pdb=" O MET A 770 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AD5, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.824A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 92 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 183 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.880A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.742A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 298 through 306 removed outlier: 7.048A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 312 through 315 Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.974A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.354A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.232A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.546A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.546A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.679A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF1, first strand: chain 'C' and resid 1102 through 1104 1009 hydrogen bonds defined for protein. 2811 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: 10.00 Time building geometry restraints manager: 9.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4552 1.33 - 1.46: 8168 1.46 - 1.59: 11184 1.59 - 1.72: 2 1.72 - 1.86: 167 Bond restraints: 24073 Sorted by residual: bond pdb=" CG PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 1.503 1.195 0.308 3.40e-02 8.65e+02 8.21e+01 bond pdb=" CG PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.503 1.196 0.307 3.40e-02 8.65e+02 8.17e+01 bond pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 1.492 1.673 -0.181 5.00e-02 4.00e+02 1.31e+01 bond pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.64e+00 ... (remaining 24068 not shown) Histogram of bond angle deviations from ideal: 84.83 - 95.30: 4 95.30 - 105.77: 512 105.77 - 116.23: 15722 116.23 - 126.70: 16236 126.70 - 137.17: 230 Bond angle restraints: 32704 Sorted by residual: angle pdb=" N PRO B 493 " pdb=" CD PRO B 493 " pdb=" CG PRO B 493 " ideal model delta sigma weight residual 103.20 84.83 18.37 1.50e+00 4.44e-01 1.50e+02 angle pdb=" N PRO A 202 " pdb=" CD PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 103.20 85.32 17.88 1.50e+00 4.44e-01 1.42e+02 angle pdb=" CA PRO A 202 " pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 112.00 96.56 15.44 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CA PRO A 202 " pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 104.50 90.33 14.17 1.90e+00 2.77e-01 5.56e+01 angle pdb=" CA PRO B 493 " pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 112.00 101.81 10.19 1.40e+00 5.10e-01 5.30e+01 ... (remaining 32699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 13682 17.55 - 35.11: 911 35.11 - 52.66: 218 52.66 - 70.21: 38 70.21 - 87.76: 14 Dihedral angle restraints: 14863 sinusoidal: 6289 harmonic: 8574 Sorted by residual: dihedral pdb=" CB CYS C 278 " pdb=" SG CYS C 278 " pdb=" SG CYS C 288 " pdb=" CB CYS C 288 " ideal model delta sinusoidal sigma weight residual -86.00 -173.76 87.76 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 288 " pdb=" CB CYS A 288 " ideal model delta sinusoidal sigma weight residual -86.00 -173.40 87.40 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA VAL B 205 " pdb=" C VAL B 205 " pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta harmonic sigma weight residual 180.00 139.26 40.74 0 5.00e+00 4.00e-02 6.64e+01 ... (remaining 14860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3681 0.115 - 0.231: 137 0.231 - 0.346: 7 0.346 - 0.461: 1 0.461 - 0.577: 2 Chirality restraints: 3828 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 318 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1056 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A1056 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 3825 not shown) Planarity restraints: 4201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 334 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 335 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 227 " -0.004 2.00e-02 2.50e+03 4.25e-02 2.26e+01 pdb=" CG ASN B 227 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 227 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN B 227 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 492 " -0.081 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO B 493 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 493 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 493 " -0.060 5.00e-02 4.00e+02 ... (remaining 4198 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4707 2.78 - 3.31: 19354 3.31 - 3.84: 36409 3.84 - 4.37: 43842 4.37 - 4.90: 77708 Nonbonded interactions: 182020 Sorted by model distance: nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.250 2.440 nonbonded pdb=" O SER A 380 " pdb=" OG1 THR A 509 " model vdw 2.263 2.440 nonbonded pdb=" O SER C 380 " pdb=" OG1 THR C 509 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 698 " pdb=" O GLN A1053 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR C 894 " pdb=" OD1 ASN C 896 " model vdw 2.309 2.440 ... (remaining 182015 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 31 through 455 or resid 477 through 1123 or resid 1301 thr \ ough 1312)) selection = (chain 'B' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 810 or resid 834 through 1123 or resid 1301 through 1312)) selection = (chain 'C' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 1123 or resid 1301 through 1312)) } 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=0.00 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.870 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 62.830 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.110 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:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.006 0.308 24073 Z= 0.365 Angle : 0.837 18.368 32704 Z= 0.469 Chirality : 0.055 0.577 3828 Planarity : 0.007 0.124 4163 Dihedral : 12.518 87.630 9217 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 2883 helix: -0.07 (0.19), residues: 695 sheet: 0.64 (0.18), residues: 741 loop : -1.97 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 PHE 0.043 0.002 PHE B 360 TYR 0.040 0.002 TYR B 440 ARG 0.006 0.001 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.7945 (m-30) cc_final: 0.7682 (m-30) REVERT: C 110 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7283 (tptt) REVERT: C 793 LYS cc_start: 0.6064 (ttpt) cc_final: 0.5834 (mtmt) REVERT: C 965 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.7558 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 1.2059 time to fit residues: 303.8080 Evaluate side-chains 153 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 96 ASN B 108 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24073 Z= 0.195 Angle : 0.548 7.632 32704 Z= 0.289 Chirality : 0.046 0.489 3828 Planarity : 0.005 0.074 4163 Dihedral : 6.919 58.039 3972 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.78 % Allowed : 5.47 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.51 (0.15), residues: 2883 helix: 1.10 (0.20), residues: 692 sheet: 0.83 (0.19), residues: 706 loop : -1.71 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.005 0.001 HIS C1046 PHE 0.022 0.002 PHE A 629 TYR 0.027 0.001 TYR A 491 ARG 0.002 0.000 ARG B 982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.7944 (m-30) cc_final: 0.7664 (m-30) REVERT: B 768 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7848 (pttm) REVERT: B 835 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: A 107 MET cc_start: 0.8347 (mmm) cc_final: 0.7959 (mmm) REVERT: C 110 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7306 (tptt) REVERT: C 965 ARG cc_start: 0.7662 (ptp-170) cc_final: 0.7457 (ptp-110) outliers start: 20 outliers final: 4 residues processed: 180 average time/residue: 1.0975 time to fit residues: 235.4763 Evaluate side-chains 153 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN B 744 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24073 Z= 0.314 Angle : 0.597 11.276 32704 Z= 0.315 Chirality : 0.049 0.504 3828 Planarity : 0.005 0.057 4163 Dihedral : 6.493 57.984 3972 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 1.52 % Allowed : 7.82 % Favored : 90.66 % 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: -0.42 (0.15), residues: 2883 helix: 1.23 (0.20), residues: 690 sheet: 0.82 (0.19), residues: 710 loop : -1.66 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 868 HIS 0.007 0.001 HIS A1030 PHE 0.023 0.002 PHE A 629 TYR 0.019 0.002 TYR C1049 ARG 0.006 0.000 ARG B 982 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.7932 (m-30) cc_final: 0.7652 (m-30) REVERT: B 768 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7832 (pttm) REVERT: B 835 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: A 107 MET cc_start: 0.8350 (mmm) cc_final: 0.7950 (mmm) REVERT: A 554 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5836 (t0) REVERT: A 727 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6891 (p0) REVERT: C 110 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7358 (tptt) REVERT: C 932 ASP cc_start: 0.7269 (m-30) cc_final: 0.6889 (m-30) REVERT: C 965 ARG cc_start: 0.7717 (ptp-170) cc_final: 0.7473 (ptp-110) outliers start: 39 outliers final: 15 residues processed: 193 average time/residue: 1.0981 time to fit residues: 252.0928 Evaluate side-chains 173 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 1074 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 138 optimal weight: 0.0050 chunk 29 optimal weight: 0.4980 chunk 127 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24073 Z= 0.146 Angle : 0.492 8.858 32704 Z= 0.259 Chirality : 0.045 0.478 3828 Planarity : 0.004 0.046 4163 Dihedral : 5.794 52.111 3972 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 9.89 % Favored : 88.82 % 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: -0.08 (0.15), residues: 2883 helix: 1.65 (0.20), residues: 688 sheet: 1.06 (0.19), residues: 695 loop : -1.51 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 423 HIS 0.004 0.000 HIS C1046 PHE 0.017 0.001 PHE A 629 TYR 0.018 0.001 TYR B1049 ARG 0.001 0.000 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.7866 (m-30) cc_final: 0.7602 (m-30) REVERT: A 107 MET cc_start: 0.8338 (mmm) cc_final: 0.7961 (mmm) REVERT: C 110 LYS cc_start: 0.7826 (ptpt) cc_final: 0.7331 (tptt) REVERT: C 321 ASN cc_start: 0.7497 (m-40) cc_final: 0.7082 (p0) REVERT: C 932 ASP cc_start: 0.7234 (m-30) cc_final: 0.6872 (m-30) REVERT: C 965 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7425 (ptp-110) outliers start: 33 outliers final: 12 residues processed: 205 average time/residue: 0.9769 time to fit residues: 242.8686 Evaluate side-chains 171 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 0.0470 chunk 160 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 254 optimal weight: 0.0470 chunk 71 optimal weight: 0.0980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN A 889 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24073 Z= 0.181 Angle : 0.512 12.967 32704 Z= 0.268 Chirality : 0.046 0.491 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.538 50.580 3972 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 1.80 % Allowed : 10.95 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.02 (0.15), residues: 2883 helix: 1.80 (0.21), residues: 688 sheet: 1.04 (0.19), residues: 706 loop : -1.46 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.004 0.001 HIS C1046 PHE 0.019 0.001 PHE A 629 TYR 0.018 0.001 TYR C1049 ARG 0.002 0.000 ARG B 982 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8353 (mm) REVERT: A 102 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 107 MET cc_start: 0.8339 (mmm) cc_final: 0.7944 (mmm) REVERT: C 110 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7329 (tptt) REVERT: C 321 ASN cc_start: 0.7525 (m-40) cc_final: 0.7190 (p0) REVERT: C 932 ASP cc_start: 0.7277 (m-30) cc_final: 0.6922 (m-30) REVERT: C 965 ARG cc_start: 0.7677 (ptp-170) cc_final: 0.7414 (ptp-110) outliers start: 46 outliers final: 22 residues processed: 202 average time/residue: 1.0043 time to fit residues: 245.3061 Evaluate side-chains 184 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 1074 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 769 GLN A 78 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24073 Z= 0.262 Angle : 0.549 10.564 32704 Z= 0.289 Chirality : 0.048 0.502 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.597 51.350 3972 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 1.95 % Allowed : 11.42 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.07 (0.15), residues: 2883 helix: 1.70 (0.20), residues: 689 sheet: 0.94 (0.19), residues: 714 loop : -1.49 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 868 HIS 0.006 0.001 HIS A1030 PHE 0.020 0.002 PHE A 629 TYR 0.023 0.001 TYR C 200 ARG 0.004 0.000 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 167 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6906 (tmm) REVERT: B 572 ASP cc_start: 0.7809 (m-30) cc_final: 0.7592 (m-30) REVERT: B 965 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (ptt180) REVERT: A 54 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 102 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7421 (m) REVERT: A 107 MET cc_start: 0.8348 (mmm) cc_final: 0.7938 (mmm) REVERT: A 554 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5716 (t0) REVERT: C 56 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: C 110 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7349 (tptt) REVERT: C 124 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7211 (m) REVERT: C 321 ASN cc_start: 0.7633 (m-40) cc_final: 0.7428 (p0) REVERT: C 762 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: C 965 ARG cc_start: 0.7695 (ptp-170) cc_final: 0.7429 (ptp-110) REVERT: C 972 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6969 (mp0) outliers start: 50 outliers final: 31 residues processed: 203 average time/residue: 1.0199 time to fit residues: 250.4749 Evaluate side-chains 194 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 161 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 172 optimal weight: 0.0980 chunk 130 optimal weight: 10.0000 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24073 Z= 0.142 Angle : 0.490 14.014 32704 Z= 0.255 Chirality : 0.045 0.480 3828 Planarity : 0.004 0.045 4163 Dihedral : 5.261 47.726 3972 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 1.72 % Allowed : 12.28 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.11 (0.15), residues: 2883 helix: 1.91 (0.20), residues: 688 sheet: 1.05 (0.19), residues: 709 loop : -1.40 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 868 HIS 0.004 0.000 HIS C1046 PHE 0.017 0.001 PHE A 629 TYR 0.017 0.001 TYR B1049 ARG 0.002 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 745 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7310 (tt) REVERT: B 965 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7705 (ptt180) REVERT: A 102 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7399 (m) REVERT: A 107 MET cc_start: 0.8338 (mmm) cc_final: 0.7947 (mmm) REVERT: A 184 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: C 110 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7318 (tptt) REVERT: C 762 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7567 (pp20) outliers start: 44 outliers final: 24 residues processed: 198 average time/residue: 1.0247 time to fit residues: 243.7765 Evaluate side-chains 182 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 769 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN A 889 ASN A 904 GLN C 409 ASN C 915 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24073 Z= 0.309 Angle : 0.573 11.794 32704 Z= 0.301 Chirality : 0.048 0.508 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.504 49.964 3972 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 1.76 % Allowed : 12.90 % Favored : 85.34 % 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: -0.08 (0.15), residues: 2883 helix: 1.68 (0.20), residues: 689 sheet: 0.93 (0.20), residues: 680 loop : -1.42 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 868 HIS 0.007 0.001 HIS A1030 PHE 0.021 0.002 PHE A 629 TYR 0.022 0.001 TYR C 200 ARG 0.011 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6999 (tmm) REVERT: B 745 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 102 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7462 (m) REVERT: A 107 MET cc_start: 0.8349 (mmm) cc_final: 0.7921 (mmm) REVERT: C 110 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7350 (tptt) REVERT: C 124 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7225 (m) REVERT: C 762 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: C 932 ASP cc_start: 0.7419 (m-30) cc_final: 0.6954 (m-30) REVERT: C 972 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7026 (mp0) outliers start: 45 outliers final: 29 residues processed: 193 average time/residue: 1.0123 time to fit residues: 236.9652 Evaluate side-chains 186 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1099 THR Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 263 optimal weight: 0.2980 chunk 158 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 237 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN A 904 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24073 Z= 0.153 Angle : 0.492 12.111 32704 Z= 0.258 Chirality : 0.045 0.477 3828 Planarity : 0.004 0.045 4163 Dihedral : 5.246 46.768 3972 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 1.41 % Allowed : 13.17 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2883 helix: 1.86 (0.20), residues: 688 sheet: 1.04 (0.19), residues: 713 loop : -1.39 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 868 HIS 0.004 0.000 HIS C1046 PHE 0.018 0.001 PHE A 629 TYR 0.022 0.001 TYR C 200 ARG 0.004 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 745 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7349 (tt) REVERT: A 102 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7405 (m) REVERT: A 107 MET cc_start: 0.8343 (mmm) cc_final: 0.7952 (mmm) REVERT: C 110 LYS cc_start: 0.7841 (ptpt) cc_final: 0.7320 (tptt) REVERT: C 762 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: C 932 ASP cc_start: 0.7318 (m-30) cc_final: 0.6947 (m-30) outliers start: 36 outliers final: 23 residues processed: 178 average time/residue: 0.9835 time to fit residues: 211.9315 Evaluate side-chains 177 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 0.0570 chunk 278 optimal weight: 0.8980 chunk 169 optimal weight: 0.0670 chunk 132 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 179 optimal weight: 0.0770 chunk 142 optimal weight: 3.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN B 835 GLN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24073 Z= 0.127 Angle : 0.469 12.480 32704 Z= 0.245 Chirality : 0.044 0.462 3828 Planarity : 0.004 0.044 4163 Dihedral : 4.943 43.633 3972 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 13.68 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.24 (0.15), residues: 2883 helix: 2.06 (0.20), residues: 693 sheet: 1.16 (0.19), residues: 682 loop : -1.31 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 868 HIS 0.003 0.000 HIS C1046 PHE 0.016 0.001 PHE A 629 TYR 0.017 0.001 TYR B1049 ARG 0.002 0.000 ARG B 965 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 745 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7275 (tt) REVERT: A 107 MET cc_start: 0.8348 (mmm) cc_final: 0.7937 (mmm) REVERT: C 110 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7298 (tptt) REVERT: C 762 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7484 (pp20) outliers start: 30 outliers final: 22 residues processed: 187 average time/residue: 1.0658 time to fit residues: 239.9577 Evaluate side-chains 179 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 232 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 42 optimal weight: 0.0060 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN B 769 GLN B 835 GLN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103682 restraints weight = 29377.128| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.14 r_work: 0.3010 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24073 Z= 0.165 Angle : 0.643 56.010 32704 Z= 0.356 Chirality : 0.046 0.467 3828 Planarity : 0.004 0.043 4163 Dihedral : 4.988 43.249 3972 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 1.45 % Allowed : 13.68 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.15), residues: 2883 helix: 2.07 (0.20), residues: 693 sheet: 1.20 (0.19), residues: 680 loop : -1.32 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 423 HIS 0.005 0.001 HIS C1046 PHE 0.039 0.001 PHE A 360 TYR 0.018 0.001 TYR C1049 ARG 0.005 0.000 ARG C 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6298.23 seconds wall clock time: 114 minutes 57.50 seconds (6897.50 seconds total)