Starting phenix.real_space_refine on Wed Nov 20 03:47:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/11_2024/7xu4_33458_trim.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17226 2.51 5 N 4425 2.21 5 O 5283 1.98 5 H 25311 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 1.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52371 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "C" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 22.34, per 1000 atoms: 0.43 Number of scatterers: 52371 At special positions: 0 Unit cell: (141.113, 151.723, 165.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5283 8.00 N 4425 7.00 C 17226 6.00 H 25311 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 17 " " NAG B1802 " - " ASN B 61 " " NAG B1803 " - " ASN B 122 " " NAG B1804 " - " ASN B 331 " " NAG B1805 " - " ASN B 603 " " NAG B1806 " - " ASN B 616 " " NAG B1807 " - " ASN B 657 " " NAG B1808 " - " ASN B 709 " " NAG B1809 " - " ASN B1074 " " NAG B1810 " - " ASN B1098 " " NAG B1811 " - " ASN B 165 " " NAG B1812 " - " ASN B 282 " " NAG B1813 " - " ASN B 343 " " NAG B1814 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1134 " Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 3.4 seconds 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6222 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 26.2% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.755A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.429A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.344A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.200A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.654A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.403A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.045A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.568A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.521A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.144A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.684A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.755A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.664A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.436A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.340A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.204A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.650A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 4.402A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 843 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.524A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.147A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.677A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.759A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.662A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.431A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.344A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.207A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.400A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.051A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.532A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.145A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.682A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.746A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.001A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 162 removed outlier: 6.223A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.560A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.229A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.332A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.271A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.772A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.772A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.299A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.627A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.741A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.997A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'C' and resid 152 through 162 removed outlier: 6.222A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.557A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.227A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.335A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.271A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.611A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.739A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.996A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.820A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 84 through 85 removed outlier: 8.113A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.561A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.237A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.335A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.268A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.351A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.621A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3039 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: 24.60 Time building geometry restraints manager: 14.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 25305 1.05 - 1.27: 4365 1.27 - 1.49: 11617 1.49 - 1.70: 11543 1.70 - 1.92: 153 Bond restraints: 52983 Sorted by residual: bond pdb=" C4C BLA B1815 " pdb=" NC BLA B1815 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" NB BLA A1314 " pdb=" C4B BLA A1314 " ideal model delta sigma weight residual 1.371 1.527 -0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" NB BLA B1815 " pdb=" C4B BLA B1815 " ideal model delta sigma weight residual 1.371 1.527 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 52978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.43: 94883 6.43 - 12.87: 61 12.87 - 19.30: 0 19.30 - 25.73: 3 25.73 - 32.17: 3 Bond angle restraints: 94950 Sorted by residual: angle pdb=" C11 EIC B1801 " pdb=" C10 EIC B1801 " pdb=" C9 EIC B1801 " ideal model delta sigma weight residual 127.32 95.15 32.17 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C11 EIC C1315 " pdb=" C10 EIC C1315 " pdb=" C9 EIC C1315 " ideal model delta sigma weight residual 127.32 95.29 32.03 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C11 EIC A1315 " pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " ideal model delta sigma weight residual 127.32 95.36 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 135.13 -20.73 2.30e+00 1.89e-01 8.13e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 135.07 -20.67 2.30e+00 1.89e-01 8.08e+01 ... (remaining 94945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23713 17.68 - 35.37: 1898 35.37 - 53.05: 555 53.05 - 70.74: 147 70.74 - 88.42: 36 Dihedral angle restraints: 26349 sinusoidal: 14709 harmonic: 11640 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.37 61.63 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.43 61.57 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.59 61.41 1 1.00e+01 1.00e-02 5.01e+01 ... (remaining 26346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3740 0.072 - 0.144: 579 0.144 - 0.216: 88 0.216 - 0.287: 3 0.287 - 0.359: 3 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4410 not shown) Planarity restraints: 8004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB BLA B1815 " 0.052 2.00e-02 2.50e+03 6.17e-02 9.51e+01 pdb=" OB BLA B1815 " -0.006 2.00e-02 2.50e+03 pdb=" C1B BLA B1815 " 0.059 2.00e-02 2.50e+03 pdb=" C2B BLA B1815 " 0.013 2.00e-02 2.50e+03 pdb=" C3B BLA B1815 " -0.016 2.00e-02 2.50e+03 pdb=" C4A BLA B1815 " -0.139 2.00e-02 2.50e+03 pdb=" C4B BLA B1815 " 0.009 2.00e-02 2.50e+03 pdb=" CAB BLA B1815 " -0.064 2.00e-02 2.50e+03 pdb=" CHB BLA B1815 " 0.089 2.00e-02 2.50e+03 pdb=" CMB BLA B1815 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A1314 " 0.052 2.00e-02 2.50e+03 6.17e-02 9.51e+01 pdb=" OB BLA A1314 " -0.006 2.00e-02 2.50e+03 pdb=" C1B BLA A1314 " 0.059 2.00e-02 2.50e+03 pdb=" C2B BLA A1314 " 0.013 2.00e-02 2.50e+03 pdb=" C3B BLA A1314 " -0.015 2.00e-02 2.50e+03 pdb=" C4A BLA A1314 " -0.139 2.00e-02 2.50e+03 pdb=" C4B BLA A1314 " 0.009 2.00e-02 2.50e+03 pdb=" CAB BLA A1314 " -0.064 2.00e-02 2.50e+03 pdb=" CHB BLA A1314 " 0.089 2.00e-02 2.50e+03 pdb=" CMB BLA A1314 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA C1314 " -0.053 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" OB BLA C1314 " 0.006 2.00e-02 2.50e+03 pdb=" C1B BLA C1314 " -0.058 2.00e-02 2.50e+03 pdb=" C2B BLA C1314 " -0.012 2.00e-02 2.50e+03 pdb=" C3B BLA C1314 " 0.015 2.00e-02 2.50e+03 pdb=" C4A BLA C1314 " 0.139 2.00e-02 2.50e+03 pdb=" C4B BLA C1314 " -0.009 2.00e-02 2.50e+03 pdb=" CAB BLA C1314 " 0.064 2.00e-02 2.50e+03 pdb=" CHB BLA C1314 " -0.089 2.00e-02 2.50e+03 pdb=" CMB BLA C1314 " -0.003 2.00e-02 2.50e+03 ... (remaining 8001 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 4019 2.22 - 2.82: 109131 2.82 - 3.41: 136683 3.41 - 4.01: 192000 4.01 - 4.60: 291856 Nonbonded interactions: 733689 Sorted by model distance: nonbonded pdb=" O ALA B 879 " pdb=" HG1 THR B 883 " model vdw 1.626 2.450 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.646 2.450 nonbonded pdb=" HH TYR A 37 " pdb=" O LEU A 54 " model vdw 1.647 2.450 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.649 2.450 nonbonded pdb=" OG SER B1051 " pdb=" HD1 HIS B1064 " model vdw 1.651 2.450 ... (remaining 733684 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 14 through 1140 or resid 1302 through 1313)) selection = (chain 'B' and (resid 14 through 1140 or resid 1802 through 1813)) selection = (chain 'C' and (resid 14 through 1140 or resid 1302 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.750 Extract box with map and model: 1.580 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 99.380 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.260 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.012 0.162 27672 Z= 0.831 Angle : 1.016 32.167 37656 Z= 0.464 Chirality : 0.053 0.359 4413 Planarity : 0.005 0.062 4791 Dihedral : 14.239 88.420 10941 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.31 % Allowed : 0.80 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3312 helix: 0.15 (0.18), residues: 765 sheet: -0.15 (0.18), residues: 750 loop : -1.68 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.006 0.001 HIS A1048 PHE 0.047 0.002 PHE C 392 TYR 0.023 0.002 TYR B 365 ARG 0.008 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8149 (tp-100) REVERT: C 153 MET cc_start: 0.8150 (ppp) cc_final: 0.7927 (ppp) outliers start: 9 outliers final: 5 residues processed: 168 average time/residue: 0.7079 time to fit residues: 187.7956 Evaluate side-chains 113 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.6980 chunk 252 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN C 14 GLN C 901 GLN B 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27672 Z= 0.198 Angle : 0.586 14.257 37656 Z= 0.304 Chirality : 0.045 0.332 4413 Planarity : 0.004 0.056 4791 Dihedral : 8.475 59.343 5040 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.59 % Allowed : 3.22 % Favored : 96.20 % 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: 3312 helix: 0.67 (0.19), residues: 777 sheet: -0.07 (0.18), residues: 750 loop : -1.55 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS B1088 PHE 0.018 0.001 PHE C 392 TYR 0.015 0.001 TYR B 365 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.7710 (t0) cc_final: 0.7489 (t0) outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 0.8556 time to fit residues: 195.1573 Evaluate side-chains 119 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 251 optimal weight: 0.1980 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 302 optimal weight: 0.0870 chunk 327 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 300 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27672 Z= 0.173 Angle : 0.553 14.001 37656 Z= 0.286 Chirality : 0.044 0.317 4413 Planarity : 0.003 0.053 4791 Dihedral : 7.603 57.758 5034 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.59 % Allowed : 4.39 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3312 helix: 0.98 (0.20), residues: 777 sheet: -0.06 (0.18), residues: 768 loop : -1.45 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS B 66 PHE 0.014 0.001 PHE A 392 TYR 0.014 0.001 TYR A 365 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 4.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 131 average time/residue: 0.8395 time to fit residues: 180.9418 Evaluate side-chains 122 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27672 Z= 0.315 Angle : 0.568 14.383 37656 Z= 0.295 Chirality : 0.045 0.310 4413 Planarity : 0.004 0.049 4791 Dihedral : 7.117 59.554 5034 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.55 % Allowed : 6.05 % Favored : 93.40 % 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: -0.83 (0.14), residues: 3312 helix: 0.94 (0.20), residues: 774 sheet: -0.09 (0.18), residues: 762 loop : -1.47 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.001 PHE A 392 TYR 0.018 0.001 TYR B 365 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8174 (pp20) cc_final: 0.7974 (pp20) outliers start: 16 outliers final: 10 residues processed: 135 average time/residue: 0.8627 time to fit residues: 190.9828 Evaluate side-chains 121 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 14 GLN C 360 ASN C 556 ASN C 901 GLN B 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 27672 Z= 0.506 Angle : 0.646 15.347 37656 Z= 0.338 Chirality : 0.048 0.321 4413 Planarity : 0.004 0.047 4791 Dihedral : 7.199 59.576 5034 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.73 % Allowed : 7.43 % Favored : 91.84 % 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: -1.08 (0.14), residues: 3312 helix: 0.64 (0.19), residues: 774 sheet: -0.28 (0.18), residues: 759 loop : -1.57 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 436 HIS 0.005 0.001 HIS B1064 PHE 0.026 0.002 PHE A 392 TYR 0.022 0.002 TYR B 365 ARG 0.004 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8202 (pp20) cc_final: 0.7971 (pp20) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.8856 time to fit residues: 196.7200 Evaluate side-chains 121 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 987 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 66 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27672 Z= 0.205 Angle : 0.562 14.102 37656 Z= 0.292 Chirality : 0.045 0.313 4413 Planarity : 0.004 0.046 4791 Dihedral : 6.852 61.049 5034 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.66 % Allowed : 7.95 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3312 helix: 0.96 (0.20), residues: 774 sheet: -0.20 (0.18), residues: 765 loop : -1.45 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C 66 PHE 0.016 0.001 PHE B 392 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8167 (pp20) cc_final: 0.7952 (pp20) outliers start: 19 outliers final: 12 residues processed: 135 average time/residue: 0.8432 time to fit residues: 186.4592 Evaluate side-chains 122 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 448 ASN C 450 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27672 Z= 0.228 Angle : 0.541 13.983 37656 Z= 0.281 Chirality : 0.044 0.301 4413 Planarity : 0.003 0.045 4791 Dihedral : 6.600 62.768 5034 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.80 % Allowed : 8.37 % Favored : 90.84 % 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: -0.73 (0.14), residues: 3312 helix: 1.10 (0.20), residues: 774 sheet: -0.15 (0.18), residues: 753 loop : -1.38 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE C 392 TYR 0.014 0.001 TYR C 365 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8097 (pp20) cc_final: 0.7889 (pp20) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.8596 time to fit residues: 188.6111 Evaluate side-chains 126 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 448 ASN A 450 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27672 Z= 0.302 Angle : 0.557 14.226 37656 Z= 0.290 Chirality : 0.044 0.306 4413 Planarity : 0.004 0.045 4791 Dihedral : 6.578 64.026 5034 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.90 % Allowed : 8.40 % Favored : 90.70 % 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: -0.76 (0.14), residues: 3312 helix: 1.10 (0.20), residues: 774 sheet: -0.18 (0.18), residues: 756 loop : -1.41 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE C 392 TYR 0.016 0.001 TYR B 365 ARG 0.002 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8106 (pp20) cc_final: 0.7892 (pp20) outliers start: 26 outliers final: 21 residues processed: 134 average time/residue: 0.8493 time to fit residues: 187.4499 Evaluate side-chains 130 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27672 Z= 0.215 Angle : 0.537 13.931 37656 Z= 0.279 Chirality : 0.044 0.299 4413 Planarity : 0.003 0.045 4791 Dihedral : 6.463 66.949 5034 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.86 % Allowed : 8.54 % Favored : 90.59 % 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: -0.68 (0.14), residues: 3312 helix: 1.16 (0.20), residues: 774 sheet: -0.14 (0.18), residues: 756 loop : -1.36 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.014 0.001 PHE C 392 TYR 0.014 0.001 TYR C 365 ARG 0.002 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 4.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 GLU cc_start: 0.8084 (pp20) cc_final: 0.7869 (pp20) outliers start: 25 outliers final: 20 residues processed: 134 average time/residue: 0.8498 time to fit residues: 188.5579 Evaluate side-chains 130 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 331 optimal weight: 3.9990 chunk 305 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 448 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 137 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27672 Z= 0.194 Angle : 0.524 13.583 37656 Z= 0.272 Chirality : 0.044 0.300 4413 Planarity : 0.003 0.047 4791 Dihedral : 6.185 70.677 5034 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.76 % Allowed : 8.71 % Favored : 90.53 % 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 (0.14), residues: 3312 helix: 1.34 (0.20), residues: 768 sheet: -0.11 (0.18), residues: 774 loop : -1.30 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.012 0.001 PHE A 392 TYR 0.013 0.001 TYR C 365 ARG 0.002 0.000 ARG C1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.7887 (tp40) cc_final: 0.7592 (tp40) REVERT: B 200 TYR cc_start: 0.7816 (m-80) cc_final: 0.7399 (m-80) REVERT: B 661 GLU cc_start: 0.8051 (pp20) cc_final: 0.7834 (pp20) outliers start: 22 outliers final: 17 residues processed: 137 average time/residue: 0.9185 time to fit residues: 209.0374 Evaluate side-chains 129 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 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 137 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 137 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078990 restraints weight = 146788.955| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.76 r_work: 0.2944 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27672 Z= 0.272 Angle : 0.542 13.872 37656 Z= 0.281 Chirality : 0.044 0.290 4413 Planarity : 0.003 0.046 4791 Dihedral : 6.204 70.276 5034 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.83 % Allowed : 8.85 % Favored : 90.32 % 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: -0.60 (0.14), residues: 3312 helix: 1.31 (0.20), residues: 768 sheet: -0.13 (0.18), residues: 762 loop : -1.32 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 392 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8742.06 seconds wall clock time: 216 minutes 55.47 seconds (13015.47 seconds total)