Starting phenix.real_space_refine on Tue Mar 19 15:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tox_26040/03_2024/7tox_26040.pdb" } resolution = 3.62 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= -0.004 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15662 2.51 5 N 4026 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24618 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7923 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "B" Number of atoms: 7923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7923 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "C" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7918 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 7 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: "P" 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: "Q" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.29, per 1000 atoms: 0.54 Number of scatterers: 24618 At special positions: 0 Unit cell: (133.92, 135, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4825 8.00 N 4026 7.00 C 15662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 9.79 Conformation dependent library (CDL) restraints added in 4.4 seconds 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 46 sheets defined 27.5% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.646A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.547A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.618A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.368A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.237A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.075A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.561A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.675A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.584A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.937A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.834A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.848A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.968A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.565A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.855A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.573A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.846A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.584A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.665A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.803A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.037A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.708A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.802A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.048A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.707A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.090A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.600A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.648A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.715A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.601A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.861A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.867A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.136A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.686A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.421A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.703A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.201A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.259A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.689A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.641A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.165A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.126A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.887A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.940A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.760A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.497A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.575A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.719A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.719A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.652A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.961A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.594A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.604A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.555A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.324A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.761A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.497A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.564A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.998A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.707A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.632A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.632A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.857A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.71 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7297 1.34 - 1.46: 4492 1.46 - 1.58: 13234 1.58 - 1.71: 0 1.71 - 1.83: 129 Bond restraints: 25152 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.489 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 25147 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.38: 325 104.38 - 112.07: 10947 112.07 - 119.76: 10432 119.76 - 127.45: 12348 127.45 - 135.14: 163 Bond angle restraints: 34215 Sorted by residual: angle pdb=" CA VAL C 622 " pdb=" CB VAL C 622 " pdb=" CG1 VAL C 622 " ideal model delta sigma weight residual 110.40 128.87 -18.47 1.70e+00 3.46e-01 1.18e+02 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 119.71 -10.64 1.52e+00 4.33e-01 4.90e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 118.78 -9.82 1.49e+00 4.50e-01 4.34e+01 angle pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " pdb=" CG PHE B 456 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 34210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14617 17.96 - 35.92: 896 35.92 - 53.88: 163 53.88 - 71.84: 53 71.84 - 89.79: 36 Dihedral angle restraints: 15765 sinusoidal: 6918 harmonic: 8847 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.03 80.03 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.65 68.65 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CA LEU A 110 " pdb=" C LEU A 110 " pdb=" N ASP A 111 " pdb=" CA ASP A 111 " ideal model delta harmonic sigma weight residual -180.00 -149.99 -30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 15762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 4058 0.289 - 0.578: 16 0.578 - 0.867: 0 0.867 - 1.155: 0 1.155 - 1.444: 1 Chirality restraints: 4075 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.20e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 ... (remaining 4072 not shown) Planarity restraints: 4388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.139 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN C 165 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.221 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.135 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" CG ASN C1074 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.223 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.140 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN B 165 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.213 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " -0.174 2.00e-02 2.50e+03 ... (remaining 4385 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12550 2.99 - 3.47: 23906 3.47 - 3.95: 40442 3.95 - 4.42: 44404 4.42 - 4.90: 74869 Nonbonded interactions: 196171 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.515 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.523 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.524 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.550 2.440 ... (remaining 196166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 622 or resid 632 through 1147 or resid 1301 thr \ ough 1311)) selection = (chain 'B' and (resid 27 through 622 or resid 632 through 1147 or resid 1301 thr \ ough 1311)) selection = chain 'C' } 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' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.030 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 67.510 Find NCS groups from input model: 1.760 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: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.014 0.080 25152 Z= 0.885 Angle : 1.755 18.471 34215 Z= 1.165 Chirality : 0.101 1.444 4075 Planarity : 0.014 0.169 4341 Dihedral : 13.093 89.795 9950 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.68 % Favored : 92.78 % Rotamer: Outliers : 1.35 % Allowed : 3.16 % Favored : 95.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 2993 helix: -0.71 (0.17), residues: 682 sheet: 0.39 (0.22), residues: 501 loop : -1.09 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.131 0.021 TRP B 353 HIS 0.014 0.003 HIS C 519 PHE 0.060 0.011 PHE C 497 TYR 0.188 0.020 TYR C 495 ARG 0.015 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 53 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 764 ASN cc_start: 0.8253 (m-40) cc_final: 0.8043 (t0) REVERT: C 474 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6513 (mp10) outliers start: 36 outliers final: 9 residues processed: 89 average time/residue: 0.3742 time to fit residues: 54.2594 Evaluate side-chains 44 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 675 GLN B 493 GLN B 641 ASN C 751 ASN C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 25152 Z= 0.181 Angle : 0.652 12.307 34215 Z= 0.347 Chirality : 0.046 0.299 4075 Planarity : 0.004 0.048 4341 Dihedral : 7.057 76.424 4552 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.58 % Favored : 96.19 % Rotamer: Outliers : 0.75 % Allowed : 4.85 % Favored : 94.39 % 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: -0.21 (0.15), residues: 2993 helix: 1.20 (0.20), residues: 688 sheet: 0.13 (0.20), residues: 627 loop : -0.80 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 104 HIS 0.006 0.001 HIS C1048 PHE 0.015 0.001 PHE A 43 TYR 0.019 0.002 TYR C 495 ARG 0.003 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7704 (tpt170) outliers start: 20 outliers final: 11 residues processed: 55 average time/residue: 0.3501 time to fit residues: 33.9901 Evaluate side-chains 41 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 334 ASN A 474 GLN A 804 GLN B 188 ASN B 422 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25152 Z= 0.419 Angle : 0.687 8.912 34215 Z= 0.358 Chirality : 0.047 0.242 4075 Planarity : 0.004 0.044 4341 Dihedral : 6.835 59.271 4544 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer: Outliers : 1.43 % Allowed : 6.09 % Favored : 92.48 % 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: -0.42 (0.15), residues: 2993 helix: 1.09 (0.20), residues: 693 sheet: -0.13 (0.20), residues: 590 loop : -0.90 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.010 0.002 HIS B1064 PHE 0.028 0.002 PHE C1089 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 32 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5834 (t70) REVERT: B 443 SER cc_start: 0.5534 (OUTLIER) cc_final: 0.4496 (p) REVERT: C 224 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 474 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6654 (mp10) outliers start: 38 outliers final: 26 residues processed: 70 average time/residue: 0.3257 time to fit residues: 40.0224 Evaluate side-chains 56 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 26 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 276 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25152 Z= 0.187 Angle : 0.541 9.850 34215 Z= 0.284 Chirality : 0.043 0.205 4075 Planarity : 0.003 0.042 4341 Dihedral : 6.159 58.043 4540 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 1.28 % Allowed : 7.34 % Favored : 91.38 % 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: -0.09 (0.15), residues: 2993 helix: 1.59 (0.20), residues: 693 sheet: -0.10 (0.20), residues: 600 loop : -0.73 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.004 0.001 HIS C 655 PHE 0.016 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 30 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8515 (ttp) cc_final: 0.8208 (ttm) REVERT: C 224 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: C 474 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6609 (mp10) outliers start: 34 outliers final: 21 residues processed: 64 average time/residue: 0.3351 time to fit residues: 38.0513 Evaluate side-chains 50 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 27 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25152 Z= 0.304 Angle : 0.577 9.497 34215 Z= 0.300 Chirality : 0.044 0.195 4075 Planarity : 0.003 0.042 4341 Dihedral : 6.130 59.373 4539 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 1.77 % Allowed : 7.60 % Favored : 90.63 % 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: -0.16 (0.15), residues: 2993 helix: 1.57 (0.20), residues: 686 sheet: -0.10 (0.19), residues: 622 loop : -0.82 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.006 0.001 HIS C 655 PHE 0.017 0.002 PHE C1089 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 31 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: C 474 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6311 (mp10) outliers start: 47 outliers final: 34 residues processed: 78 average time/residue: 0.3396 time to fit residues: 46.1730 Evaluate side-chains 63 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 27 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25152 Z= 0.162 Angle : 0.508 10.153 34215 Z= 0.265 Chirality : 0.042 0.159 4075 Planarity : 0.003 0.040 4341 Dihedral : 5.796 57.523 4539 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 1.62 % Allowed : 8.28 % Favored : 90.11 % 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: 0.02 (0.15), residues: 2993 helix: 1.83 (0.20), residues: 688 sheet: -0.02 (0.20), residues: 627 loop : -0.74 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS C 655 PHE 0.016 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 27 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 1084 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7872 (p0) REVERT: B 697 MET cc_start: 0.8577 (ttp) cc_final: 0.8376 (ttm) REVERT: C 224 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: C 474 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6227 (mp10) outliers start: 43 outliers final: 30 residues processed: 70 average time/residue: 0.3123 time to fit residues: 39.3696 Evaluate side-chains 61 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 27 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 165 optimal weight: 0.1980 chunk 246 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 292 optimal weight: 0.0030 chunk 182 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25152 Z= 0.203 Angle : 0.524 12.836 34215 Z= 0.273 Chirality : 0.042 0.156 4075 Planarity : 0.003 0.040 4341 Dihedral : 5.715 57.054 4539 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 1.66 % Allowed : 8.62 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2993 helix: 1.89 (0.20), residues: 688 sheet: 0.03 (0.20), residues: 633 loop : -0.73 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS C 655 PHE 0.022 0.001 PHE C 392 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 28 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 1084 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 697 MET cc_start: 0.8650 (ttp) cc_final: 0.8447 (ttm) REVERT: C 224 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: C 474 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6206 (mp10) outliers start: 44 outliers final: 35 residues processed: 71 average time/residue: 0.3227 time to fit residues: 41.3579 Evaluate side-chains 66 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 27 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 144 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 229 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25152 Z= 0.256 Angle : 0.537 9.602 34215 Z= 0.279 Chirality : 0.043 0.291 4075 Planarity : 0.003 0.040 4341 Dihedral : 5.724 57.794 4539 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 1.58 % Allowed : 8.95 % Favored : 89.47 % 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: -0.01 (0.15), residues: 2993 helix: 1.77 (0.20), residues: 695 sheet: -0.03 (0.19), residues: 631 loop : -0.76 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.007 0.001 HIS C 519 PHE 0.020 0.001 PHE C 392 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 27 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8820 (p) REVERT: A 1084 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7784 (p0) REVERT: C 224 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8318 (pm20) outliers start: 42 outliers final: 36 residues processed: 69 average time/residue: 0.3142 time to fit residues: 39.4945 Evaluate side-chains 66 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 27 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 6.9990 chunk 279 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 257 optimal weight: 0.0470 chunk 271 optimal weight: 1.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25152 Z= 0.141 Angle : 0.486 9.500 34215 Z= 0.254 Chirality : 0.042 0.276 4075 Planarity : 0.003 0.040 4341 Dihedral : 5.357 57.365 4539 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 1.28 % Allowed : 9.33 % Favored : 89.39 % 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: 0.21 (0.15), residues: 2993 helix: 2.10 (0.21), residues: 683 sheet: 0.13 (0.19), residues: 641 loop : -0.69 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS B1048 PHE 0.017 0.001 PHE C 392 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 29 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 581 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (p) REVERT: A 1084 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7742 (p0) REVERT: C 224 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8288 (pm20) outliers start: 34 outliers final: 28 residues processed: 63 average time/residue: 0.3671 time to fit residues: 41.3098 Evaluate side-chains 59 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 27 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 240 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25152 Z= 0.210 Angle : 0.504 9.450 34215 Z= 0.262 Chirality : 0.042 0.274 4075 Planarity : 0.003 0.054 4341 Dihedral : 5.334 57.600 4537 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 9.37 % Favored : 89.32 % 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: 0.19 (0.15), residues: 2993 helix: 2.04 (0.20), residues: 683 sheet: 0.13 (0.19), residues: 643 loop : -0.69 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.004 0.001 HIS C 655 PHE 0.015 0.001 PHE C 392 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 27 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 1084 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 319 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6823 (mmm160) REVERT: C 224 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8277 (pm20) outliers start: 35 outliers final: 28 residues processed: 61 average time/residue: 0.3369 time to fit residues: 36.5803 Evaluate side-chains 59 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 27 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038828 restraints weight = 155363.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039608 restraints weight = 97500.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040053 restraints weight = 60843.493| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25152 Z= 0.183 Angle : 0.488 9.411 34215 Z= 0.254 Chirality : 0.042 0.266 4075 Planarity : 0.003 0.052 4341 Dihedral : 5.254 57.385 4537 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 1.43 % Allowed : 9.26 % Favored : 89.32 % 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: 0.23 (0.15), residues: 2993 helix: 2.10 (0.20), residues: 682 sheet: 0.16 (0.19), residues: 653 loop : -0.68 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 633 HIS 0.003 0.001 HIS C 655 PHE 0.014 0.001 PHE C 392 TYR 0.019 0.001 TYR C1067 ARG 0.008 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.89 seconds wall clock time: 59 minutes 7.34 seconds (3547.34 seconds total)