Starting phenix.real_space_refine (version: dev) on Fri Feb 24 03:43:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35534 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h16_34426/02_2023/8h16_34426.pdb" } resolution = 3.35534 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 850": "OD1" <-> "OD2" Residue "B ASP 961": "OD1" <-> "OD2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1074": "OE1" <-> "OE2" Residue "B ASP 1100": "OD1" <-> "OD2" Residue "B TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" 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 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 932": "OD1" <-> "OD2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 1054": "OE1" <-> "OE2" Residue "A PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 727": "OD1" <-> "OD2" Residue "C TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 850": "OD1" <-> "OD2" Residue "C ASP 932": "OD1" <-> "OD2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1109": "OD1" <-> "OD2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21934 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7549 Classifications: {'peptide': 966} Link IDs: {'PTRANS': 44, 'TRANS': 921} Chain breaks: 11 Chain: "A" Number of atoms: 6252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6252 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 35, 'TRANS': 769} Chain breaks: 8 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7685 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 44, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 12 Time building chain proxies: 11.78, per 1000 atoms: 0.54 Number of scatterers: 21934 At special positions: 0 Unit cell: (128.25, 129.6, 163.35, 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 111 16.00 O 4243 8.00 N 3603 7.00 C 13977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 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=2.05 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A1080 " " NAG A1302 " - " ASN A 119 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 227 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 602 " " NAG A1307 " - " ASN A 691 " " NAG A1308 " - " ASN A 699 " " NAG A1309 " - " ASN A 783 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A1116 " " NAG B1301 " - " ASN B1080 " " NAG B1302 " - " ASN B 269 " " NAG B1303 " - " ASN B 318 " " NAG B1304 " - " ASN B 602 " " NAG B1305 " - " ASN B 691 " " NAG B1306 " - " ASN B 699 " " NAG B1307 " - " ASN B 783 " " NAG B1308 " - " ASN B1056 " " NAG B1309 " - " 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 " Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 3.2 seconds 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 42 sheets defined 26.8% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.164A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.990A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.277A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.213A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.929A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.580A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.859A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) 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: 3.992A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.559A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.551A pdb=" N TYR B 855 " --> pdb=" O MET B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 removed outlier: 4.408A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.875A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.348A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.040A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.819A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1014 removed outlier: 3.633A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) removed outlier: 3.660A 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 602 through 612 removed outlier: 4.134A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 740 through 765 removed outlier: 4.014A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.697A 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 868 through 873 removed outlier: 4.307A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.779A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.364A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.510A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.537A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.582A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.110A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.982A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.939A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.068A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 removed outlier: 3.591A pdb=" N GLY C 739 " --> pdb=" O LEU C 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 736 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.930A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.526A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.595A pdb=" N TYR C 855 " --> pdb=" O MET C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.746A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.184A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.525A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 943 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.529A pdb=" N LEU C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.362A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.774A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 182 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N ASN B 214 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.135A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.881A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 232 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 234 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 125 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.512A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.769A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.666A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 379 removed outlier: 3.539A pdb=" N VAL B 510 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.698A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AB2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.668A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.668A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.603A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 769 through 771 removed outlier: 5.716A pdb=" N MET B 770 " --> pdb=" O SER A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB8, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.703A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.510A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.139A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.656A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 312 through 315 removed outlier: 5.318A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.589A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.649A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AC7, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AC8, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC9, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD1, first strand: chain 'A' and resid 1076 through 1080 Processing sheet with id=AD2, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.886A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.902A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.471A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 298 through 305 removed outlier: 3.694A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.712A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.603A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AD9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE1, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.521A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.561A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.561A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE6, first strand: chain 'C' and resid 1102 through 1104 932 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6987 1.35 - 1.47: 5787 1.47 - 1.60: 9467 1.60 - 1.72: 0 1.72 - 1.85: 152 Bond restraints: 22393 Sorted by residual: bond pdb=" CB CYS C 635 " pdb=" SG CYS C 635 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.61e+00 bond pdb=" CB VAL B1047 " pdb=" CG1 VAL B1047 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.48e+00 bond pdb=" C PHE C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.25e-02 6.40e+03 2.89e+00 bond pdb=" CA CYS B 511 " pdb=" CB CYS B 511 " ideal model delta sigma weight residual 1.533 1.506 0.027 1.65e-02 3.67e+03 2.60e+00 bond pdb=" C THR A 616 " pdb=" N PRO A 617 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.59e+00 ... (remaining 22388 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.80: 409 104.80 - 112.40: 11406 112.40 - 120.00: 8010 120.00 - 127.59: 10437 127.59 - 135.19: 150 Bond angle restraints: 30412 Sorted by residual: angle pdb=" CA PRO B 218 " pdb=" N PRO B 218 " pdb=" CD PRO B 218 " ideal model delta sigma weight residual 112.00 104.25 7.75 1.40e+00 5.10e-01 3.06e+01 angle pdb=" C ILE C 652 " pdb=" N GLY C 653 " pdb=" CA GLY C 653 " ideal model delta sigma weight residual 122.54 115.60 6.94 1.35e+00 5.49e-01 2.64e+01 angle pdb=" C GLY C 653 " pdb=" N ALA C 654 " pdb=" CA ALA C 654 " ideal model delta sigma weight residual 122.40 128.75 -6.35 1.45e+00 4.76e-01 1.92e+01 angle pdb=" C LYS B 817 " pdb=" N GLN B 818 " pdb=" CA GLN B 818 " ideal model delta sigma weight residual 122.61 129.32 -6.71 1.56e+00 4.11e-01 1.85e+01 angle pdb=" N CYS B 511 " pdb=" CA CYS B 511 " pdb=" C CYS B 511 " ideal model delta sigma weight residual 108.79 115.34 -6.55 1.53e+00 4.27e-01 1.83e+01 ... (remaining 30407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12118 17.99 - 35.97: 965 35.97 - 53.96: 156 53.96 - 71.94: 46 71.94 - 89.93: 12 Dihedral angle restraints: 13297 sinusoidal: 5290 harmonic: 8007 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -17.77 -68.23 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS A1064 " pdb=" SG CYS A1064 " pdb=" SG CYS A1108 " pdb=" CB CYS A1108 " ideal model delta sinusoidal sigma weight residual -86.00 -19.04 -66.96 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 13294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3440 0.119 - 0.238: 118 0.238 - 0.357: 4 0.357 - 0.476: 3 0.476 - 0.595: 1 Chirality restraints: 3566 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1056 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A1080 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 3563 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 217 " -0.101 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO B 218 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " 0.055 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO B 82 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 790 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO A 791 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 791 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 791 " 0.039 5.00e-02 4.00e+02 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3247 2.76 - 3.29: 18603 3.29 - 3.83: 32782 3.83 - 4.36: 39067 4.36 - 4.90: 71728 Nonbonded interactions: 165427 Sorted by model distance: nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.223 2.440 nonbonded pdb=" O ASP A 932 " pdb=" NE2 GLN A 936 " model vdw 2.238 2.520 nonbonded pdb=" OG SER B 685 " pdb=" OE1 GLN C 769 " model vdw 2.243 2.440 nonbonded pdb=" NZ LYS B 390 " pdb=" OD2 ASP B 392 " model vdw 2.281 2.520 nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.287 2.440 ... (remaining 165422 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 'B' selection = (chain 'C' and (resid 31 through 118 or resid 123 through 129 or resid 163 throu \ gh 1123 or resid 1301 through 1309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 13977 2.51 5 N 3603 2.21 5 O 4243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.300 Process input model: 55.730 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 0.075 22393 Z= 0.393 Angle : 0.840 12.780 30412 Z= 0.483 Chirality : 0.056 0.595 3566 Planarity : 0.007 0.149 3873 Dihedral : 13.424 89.929 8031 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 2690 helix: -0.60 (0.19), residues: 633 sheet: 0.95 (0.21), residues: 577 loop : -1.37 (0.13), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.536 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3419 time to fit residues: 116.3730 Evaluate side-chains 178 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 214 optimal weight: 0.0970 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN B 904 GLN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS C 883 GLN C 915 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 22393 Z= 0.147 Angle : 0.498 7.757 30412 Z= 0.267 Chirality : 0.045 0.519 3566 Planarity : 0.005 0.084 3873 Dihedral : 4.760 26.435 3131 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2690 helix: 0.84 (0.21), residues: 637 sheet: 0.99 (0.20), residues: 598 loop : -1.14 (0.14), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 210 average time/residue: 0.3257 time to fit residues: 109.6381 Evaluate side-chains 196 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2030 time to fit residues: 9.2430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 169 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN B 907 ASN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN C 915 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 22393 Z= 0.304 Angle : 0.571 7.469 30412 Z= 0.306 Chirality : 0.048 0.493 3566 Planarity : 0.005 0.067 3873 Dihedral : 4.917 28.599 3131 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2690 helix: 0.93 (0.21), residues: 646 sheet: 0.94 (0.20), residues: 594 loop : -1.22 (0.14), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 213 average time/residue: 0.3486 time to fit residues: 119.2971 Evaluate side-chains 194 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2083 time to fit residues: 9.9875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22393 Z= 0.210 Angle : 0.511 7.256 30412 Z= 0.272 Chirality : 0.046 0.498 3566 Planarity : 0.004 0.058 3873 Dihedral : 4.659 28.277 3131 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2690 helix: 1.20 (0.21), residues: 651 sheet: 0.87 (0.20), residues: 622 loop : -1.22 (0.14), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 216 average time/residue: 0.3437 time to fit residues: 118.7021 Evaluate side-chains 194 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 2.799 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2485 time to fit residues: 9.9831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 226 optimal weight: 0.0770 chunk 183 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 22393 Z= 0.415 Angle : 0.644 14.648 30412 Z= 0.342 Chirality : 0.050 0.484 3566 Planarity : 0.005 0.055 3873 Dihedral : 5.140 28.663 3131 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 2690 helix: 0.78 (0.21), residues: 645 sheet: 0.60 (0.20), residues: 618 loop : -1.40 (0.14), residues: 1427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 220 average time/residue: 0.3399 time to fit residues: 119.2185 Evaluate side-chains 201 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1933 time to fit residues: 11.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 22393 Z= 0.161 Angle : 0.501 12.792 30412 Z= 0.265 Chirality : 0.045 0.504 3566 Planarity : 0.004 0.050 3873 Dihedral : 4.585 26.061 3131 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2690 helix: 1.29 (0.21), residues: 656 sheet: 0.74 (0.20), residues: 608 loop : -1.23 (0.14), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 207 average time/residue: 0.3360 time to fit residues: 110.7791 Evaluate side-chains 190 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 2.372 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2486 time to fit residues: 7.8409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 193 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1117 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22393 Z= 0.182 Angle : 0.501 11.650 30412 Z= 0.264 Chirality : 0.045 0.488 3566 Planarity : 0.004 0.049 3873 Dihedral : 4.498 28.496 3131 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2690 helix: 1.51 (0.21), residues: 647 sheet: 0.81 (0.20), residues: 609 loop : -1.23 (0.14), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 199 average time/residue: 0.3528 time to fit residues: 111.4398 Evaluate side-chains 182 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 2.732 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2055 time to fit residues: 5.6412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 889 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22393 Z= 0.211 Angle : 0.515 10.947 30412 Z= 0.271 Chirality : 0.045 0.494 3566 Planarity : 0.004 0.048 3873 Dihedral : 4.530 28.698 3131 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2690 helix: 1.45 (0.21), residues: 651 sheet: 0.77 (0.20), residues: 619 loop : -1.26 (0.14), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 200 average time/residue: 0.3609 time to fit residues: 114.6845 Evaluate side-chains 195 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 2.492 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2462 time to fit residues: 9.0746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 22393 Z= 0.210 Angle : 0.515 10.099 30412 Z= 0.271 Chirality : 0.045 0.489 3566 Planarity : 0.004 0.047 3873 Dihedral : 4.520 28.835 3131 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2690 helix: 1.49 (0.21), residues: 647 sheet: 0.81 (0.20), residues: 615 loop : -1.28 (0.14), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 202 average time/residue: 0.3405 time to fit residues: 109.5161 Evaluate side-chains 193 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 2.468 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2011 time to fit residues: 6.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 180 optimal weight: 0.4980 chunk 272 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 889 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22393 Z= 0.196 Angle : 0.506 9.069 30412 Z= 0.266 Chirality : 0.045 0.485 3566 Planarity : 0.004 0.046 3873 Dihedral : 4.482 28.814 3131 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2690 helix: 1.53 (0.21), residues: 644 sheet: 0.87 (0.20), residues: 607 loop : -1.26 (0.14), residues: 1439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 193 average time/residue: 0.3618 time to fit residues: 110.5910 Evaluate side-chains 186 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 2.266 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3992 time to fit residues: 4.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.143091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.113129 restraints weight = 25891.794| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.72 r_work: 0.2818 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 22393 Z= 0.248 Angle : 0.536 8.872 30412 Z= 0.283 Chirality : 0.046 0.481 3566 Planarity : 0.004 0.047 3873 Dihedral : 4.617 29.172 3131 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2690 helix: 1.40 (0.21), residues: 637 sheet: 0.80 (0.20), residues: 615 loop : -1.35 (0.14), residues: 1438 =============================================================================== Job complete usr+sys time: 3637.51 seconds wall clock time: 67 minutes 22.16 seconds (4042.16 seconds total)