Starting phenix.real_space_refine on Fri Aug 9 07:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/08_2024/8h0y_34418.cif" } resolution = 2.85 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= 0.006 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 141 5.16 5 C 15977 2.51 5 N 4056 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 762": "OE1" <-> "OE2" Residue "B TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C ASP 684": "OD1" <-> "OD2" Residue "C ASP 727": "OD1" <-> "OD2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C GLU 970": "OE1" <-> "OE2" Residue "C GLU 1054": "OE1" <-> "OE2" 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-5409/modules/chem_data/mon_lib" Total number of atoms: 24999 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7974 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 49, 'TRANS': 969} Chain breaks: 9 Chain: "A" Number of atoms: 8143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8143 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 50, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8049 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 49, 'TRANS': 981} Chain breaks: 6 Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 13.23, per 1000 atoms: 0.53 Number of scatterers: 24999 At special positions: 0 Unit cell: (121.545, 125.925, 174.105, 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 141 16.00 O 4825 8.00 N 4056 7.00 C 15977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.05 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 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 A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.05 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.07 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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 A1302 " - " ASN A1056 " " NAG A1303 " - " ASN A 65 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A 109 " " NAG A1306 " - " ASN A 119 " " NAG A1307 " - " ASN A 158 " " NAG A1308 " - " ASN A 227 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 318 " " NAG A1311 " - " ASN A 330 " " NAG A1312 " - " ASN A 357 " " NAG A1313 " - " ASN A 602 " " NAG A1314 " - " ASN A 699 " " NAG A1315 " - " ASN A 783 " " NAG A1316 " - " ASN A1116 " " NAG B1302 " - " ASN B1056 " " NAG B1303 " - " ASN B 65 " " NAG B1304 " - " ASN B1080 " " NAG B1305 " - " ASN B 109 " " NAG B1306 " - " ASN B 119 " " NAG B1307 " - " ASN B 158 " " NAG B1308 " - " ASN B 227 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 318 " " NAG B1311 " - " ASN B 330 " " NAG B1312 " - " ASN B 357 " " NAG B1313 " - " ASN B 602 " " NAG B1314 " - " ASN B 691 " " NAG B1315 " - " ASN B 699 " " NAG B1316 " - " ASN B 783 " " NAG B1317 " - " ASN B1116 " " NAG C1302 " - " ASN C1056 " " NAG C1303 " - " ASN C 65 " " NAG C1304 " - " ASN C1080 " " NAG C1305 " - " ASN C 109 " " NAG C1306 " - " ASN C 119 " " NAG C1307 " - " ASN C 158 " " NAG C1308 " - " ASN C 227 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 318 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 602 " " NAG C1313 " - " ASN C 691 " " NAG C1314 " - " ASN C 699 " " NAG C1315 " - " ASN C 783 " " NAG C1316 " - " ASN C1116 " Time building additional restraints: 8.41 Conformation dependent library (CDL) restraints added in 4.3 seconds 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 44 sheets defined 26.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.513A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.658A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.555A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.278A 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 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 739 through 765 removed outlier: 4.465A pdb=" N THR B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.738A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 838 removed outlier: 3.604A pdb=" N ASN B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.855A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.666A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 965 removed outlier: 3.829A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.621A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.682A pdb=" N VAL A 354 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.752A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.665A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 739 through 765 removed outlier: 4.026A pdb=" N THR A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.529A 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: 3.792A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 830 through 837 removed outlier: 3.514A pdb=" N ALA A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 868 through 873 removed outlier: 4.504A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.759A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.758A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 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: 3.775A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.896A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.512A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.764A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.760A pdb=" N LEU C 355 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.558A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.513A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.686A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 765 removed outlier: 3.931A pdb=" N THR C 743 " --> pdb=" O GLY C 739 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.600A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 818 through 824 Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.556A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.226A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (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 964 removed outlier: 3.823A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.600A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.360A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 93 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.033A 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: 3.912A 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: 3.727A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.642A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.809A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.162A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.633A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 3.606A 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: 6.568A 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 removed outlier: 6.798A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.752A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.752A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.557A 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: 4.443A 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 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 34 removed outlier: 7.394A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 93 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.963A 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: 7.162A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AC3, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.514A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.232A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.667A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 510 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AC7, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.384A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.634A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.634A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.499A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 769 through 771 removed outlier: 3.657A pdb=" N SER C 685 " --> pdb=" O MET A 770 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 34 removed outlier: 7.552A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.023A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.767A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AD9, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.458A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.175A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.585A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 435 through 441 removed outlier: 5.900A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.428A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.549A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.074A 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=AE6, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.549A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.520A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1102 through 1104 1026 hydrogen bonds defined for protein. 2817 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: 10.71 Time building geometry restraints manager: 9.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 4683 1.33 - 1.48: 10003 1.48 - 1.63: 10687 1.63 - 1.78: 22 1.78 - 1.93: 167 Bond restraints: 25562 Sorted by residual: bond pdb=" ND BLA B1318 " pdb=" C1D BLA B1318 " ideal model delta sigma weight residual 1.319 1.484 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" ND BLA C1317 " pdb=" C1D BLA C1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C1C BLA B1318 " pdb=" NC BLA B1318 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" ND BLA A1317 " pdb=" C1D BLA A1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4C BLA C1317 " pdb=" NC BLA C1317 " ideal model delta sigma weight residual 1.375 1.535 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 25557 not shown) Histogram of bond angle deviations from ideal: 98.18 - 106.41: 657 106.41 - 114.63: 14970 114.63 - 122.85: 16355 122.85 - 131.07: 2712 131.07 - 139.29: 50 Bond angle restraints: 34744 Sorted by residual: angle pdb=" CA CYS C 366 " pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 114.40 139.29 -24.89 2.30e+00 1.89e-01 1.17e+02 angle pdb=" CA CYS B 159 " pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " ideal model delta sigma weight residual 114.40 132.91 -18.51 2.30e+00 1.89e-01 6.48e+01 angle pdb=" C CYS A 467 " pdb=" N THR A 468 " pdb=" CA THR A 468 " ideal model delta sigma weight residual 120.49 128.80 -8.31 1.42e+00 4.96e-01 3.42e+01 angle pdb=" N CYS C 366 " pdb=" CA CYS C 366 " pdb=" C CYS C 366 " ideal model delta sigma weight residual 108.96 116.53 -7.57 1.49e+00 4.50e-01 2.58e+01 angle pdb=" C ASN B 158 " pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 122.81 114.43 8.38 1.68e+00 3.54e-01 2.49e+01 ... (remaining 34739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14379 17.99 - 35.97: 1134 35.97 - 53.96: 245 53.96 - 71.94: 58 71.94 - 89.93: 16 Dihedral angle restraints: 15832 sinusoidal: 6822 harmonic: 9010 Sorted by residual: dihedral pdb=" CB CYS C1064 " pdb=" SG CYS C1064 " pdb=" SG CYS C1108 " pdb=" CB CYS C1108 " ideal model delta sinusoidal sigma weight residual -86.00 -0.55 -85.45 1 1.00e+01 1.00e-02 8.84e+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 -3.97 -82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual -86.00 -5.56 -80.44 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 15829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3551 0.088 - 0.176: 448 0.176 - 0.264: 14 0.264 - 0.352: 6 0.352 - 0.440: 8 Chirality restraints: 4027 Sorted by residual: chirality pdb=" C1 NAG B1315 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1315 " pdb=" O5 NAG B1315 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C1 NAG A1314 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1314 " pdb=" O5 NAG A1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB ILE C 152 " pdb=" CA ILE C 152 " pdb=" CG1 ILE C 152 " pdb=" CG2 ILE C 152 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 4024 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1318 " -0.223 2.00e-02 2.50e+03 2.75e-01 1.89e+03 pdb=" C1A BLA B1318 " 0.643 2.00e-02 2.50e+03 pdb=" C1D BLA B1318 " -0.037 2.00e-02 2.50e+03 pdb=" C2D BLA B1318 " 0.061 2.00e-02 2.50e+03 pdb=" C3D BLA B1318 " -0.071 2.00e-02 2.50e+03 pdb=" C4D BLA B1318 " -0.252 2.00e-02 2.50e+03 pdb=" CAD BLA B1318 " -0.026 2.00e-02 2.50e+03 pdb=" CHA BLA B1318 " -0.393 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " 0.046 2.00e-02 2.50e+03 pdb=" CMD BLA B1318 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1318 " -0.021 2.00e-02 2.50e+03 1.46e-01 5.30e+02 pdb=" C1D BLA B1318 " 0.331 2.00e-02 2.50e+03 pdb=" C2C BLA B1318 " 0.031 2.00e-02 2.50e+03 pdb=" C3C BLA B1318 " -0.030 2.00e-02 2.50e+03 pdb=" C4C BLA B1318 " -0.132 2.00e-02 2.50e+03 pdb=" CAC BLA B1318 " 0.000 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " -0.212 2.00e-02 2.50e+03 pdb=" CMC BLA B1318 " 0.146 2.00e-02 2.50e+03 pdb=" NC BLA B1318 " -0.127 2.00e-02 2.50e+03 pdb=" OC BLA B1318 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1317 " -0.098 2.00e-02 2.50e+03 1.12e-01 3.11e+02 pdb=" C1A BLA C1317 " 0.253 2.00e-02 2.50e+03 pdb=" C1D BLA C1317 " -0.021 2.00e-02 2.50e+03 pdb=" C2D BLA C1317 " 0.028 2.00e-02 2.50e+03 pdb=" C3D BLA C1317 " -0.023 2.00e-02 2.50e+03 pdb=" C4D BLA C1317 " -0.101 2.00e-02 2.50e+03 pdb=" CAD BLA C1317 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1317 " -0.162 2.00e-02 2.50e+03 pdb=" CHD BLA C1317 " 0.005 2.00e-02 2.50e+03 pdb=" CMD BLA C1317 " 0.111 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6275 2.80 - 3.32: 19982 3.32 - 3.85: 38803 3.85 - 4.37: 46179 4.37 - 4.90: 82281 Nonbonded interactions: 193520 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A 894 " pdb=" OD1 ASN A 896 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.312 3.040 nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 463 " model vdw 2.315 3.040 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 964 " model vdw 2.323 3.040 ... (remaining 193515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 93 or resid 96 through 250 or resid 252 through \ 603 or resid 619 through 810 or resid 815 through 823 or resid 829 through 1123 \ or resid 1301 through 1316)) selection = (chain 'B' and (resid 31 through 1123 or resid 1301 through 1316)) selection = (chain 'C' and (resid 31 through 93 or resid 96 through 250 or resid 252 through \ 810 or resid 815 through 823 or resid 829 through 1123 or resid 1301 through 13 \ 16)) } 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: 8.550 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: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 65.840 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.100 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.008 0.165 25562 Z= 0.497 Angle : 0.852 24.890 34744 Z= 0.444 Chirality : 0.057 0.440 4027 Planarity : 0.008 0.275 4422 Dihedral : 13.440 89.931 9901 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.19 (0.14), residues: 3046 helix: -0.24 (0.19), residues: 697 sheet: 0.66 (0.19), residues: 695 loop : -1.75 (0.13), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 423 HIS 0.006 0.001 HIS B 661 PHE 0.053 0.002 PHE A 334 TYR 0.023 0.002 TYR C 481 ARG 0.018 0.001 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8231 (pttm) cc_final: 0.7432 (mmtt) outliers start: 0 outliers final: 2 residues processed: 203 average time/residue: 1.2328 time to fit residues: 293.8495 Evaluate side-chains 154 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 643 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 984 GLN A 112 GLN A 122 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25562 Z= 0.232 Angle : 0.564 13.452 34744 Z= 0.301 Chirality : 0.048 0.324 4027 Planarity : 0.005 0.057 4422 Dihedral : 7.915 81.824 4415 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.12 % Allowed : 6.16 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3046 helix: 0.73 (0.20), residues: 692 sheet: 0.85 (0.19), residues: 691 loop : -1.57 (0.13), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 423 HIS 0.004 0.001 HIS A1030 PHE 0.025 0.001 PHE A 334 TYR 0.021 0.001 TYR B1049 ARG 0.006 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 976 ASP cc_start: 0.7400 (m-30) cc_final: 0.6850 (m-30) REVERT: A 606 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8032 (t) outliers start: 30 outliers final: 4 residues processed: 191 average time/residue: 1.2054 time to fit residues: 273.8843 Evaluate side-chains 156 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN A 987 GLN C 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0995 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: