Starting phenix.real_space_refine on Sun Mar 10 14:46:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu4_33458/03_2024/7xu4_33458_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17226 2.51 5 N 4425 2.21 5 O 5283 1.98 5 H 25311 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52371 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "C" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.84, per 1000 atoms: 0.32 Number of scatterers: 52371 At special positions: 0 Unit cell: (141.113, 151.723, 165.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5283 8.00 N 4425 7.00 C 17226 6.00 H 25311 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 17 " " NAG B1802 " - " ASN B 61 " " NAG B1803 " - " ASN B 122 " " NAG B1804 " - " ASN B 331 " " NAG B1805 " - " ASN B 603 " " NAG B1806 " - " ASN B 616 " " NAG B1807 " - " ASN B 657 " " NAG B1808 " - " ASN B 709 " " NAG B1809 " - " ASN B1074 " " NAG B1810 " - " ASN B1098 " " NAG B1811 " - " ASN B 165 " " NAG B1812 " - " ASN B 282 " " NAG B1813 " - " ASN B 343 " " NAG B1814 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1134 " Time building additional restraints: 30.35 Conformation dependent library (CDL) restraints added in 3.9 seconds 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 48 sheets defined 22.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.200A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 620 through 623 No H-bonds generated for 'chain 'A' and resid 620 through 623' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 637 removed outlier: 4.403A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 839 through 842 No H-bonds generated for 'chain 'A' and resid 839 through 842' Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.622A pdb=" N GLU A 918 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS A 921 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 922 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU A 938 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 940 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.684A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.204A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 620 through 623 No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 637 removed outlier: 4.402A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 839 through 842 No H-bonds generated for 'chain 'C' and resid 839 through 842' Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.617A pdb=" N GLU C 918 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS C 921 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 922 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU C 938 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 940 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.677A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.207A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 637 removed outlier: 4.400A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 839 through 842 No H-bonds generated for 'chain 'B' and resid 839 through 842' Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.619A pdb=" N GLU B 918 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS B 921 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 922 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU B 938 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 940 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.682A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.746A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.001A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.645A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= F, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.267A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.229A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.754A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.560A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 691 through 696 removed outlier: 5.772A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.020A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.299A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= O, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= P, first strand: chain 'A' and resid 711 through 717 removed outlier: 6.681A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.741A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.997A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= T, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.643A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= V, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.259A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.227A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.742A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= Z, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.557A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.782A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.047A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AE, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= AF, first strand: chain 'C' and resid 711 through 717 removed outlier: 6.676A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.739A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.996A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= AJ, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.620A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= AL, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.234A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.237A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.741A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= AP, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.561A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 691 through 696 removed outlier: 5.783A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.031A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AT, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AU, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AV, first strand: chain 'B' and resid 711 through 717 removed outlier: 6.686A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2445 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: 19.99 Time building geometry restraints manager: 32.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 25305 1.05 - 1.27: 4365 1.27 - 1.49: 11617 1.49 - 1.70: 11543 1.70 - 1.92: 153 Bond restraints: 52983 Sorted by residual: bond pdb=" C4C BLA B1815 " pdb=" NC BLA B1815 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" NB BLA A1314 " pdb=" C4B BLA A1314 " ideal model delta sigma weight residual 1.371 1.527 -0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" NB BLA B1815 " pdb=" C4B BLA B1815 " ideal model delta sigma weight residual 1.371 1.527 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 52978 not shown) Histogram of bond angle deviations from ideal: 95.15 - 103.15: 136 103.15 - 111.15: 55696 111.15 - 119.14: 15465 119.14 - 127.14: 23343 127.14 - 135.13: 310 Bond angle restraints: 94950 Sorted by residual: angle pdb=" C11 EIC B1801 " pdb=" C10 EIC B1801 " pdb=" C9 EIC B1801 " ideal model delta sigma weight residual 127.32 95.15 32.17 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C11 EIC C1315 " pdb=" C10 EIC C1315 " pdb=" C9 EIC C1315 " ideal model delta sigma weight residual 127.32 95.29 32.03 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C11 EIC A1315 " pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " ideal model delta sigma weight residual 127.32 95.36 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 135.13 -20.73 2.30e+00 1.89e-01 8.13e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 135.07 -20.67 2.30e+00 1.89e-01 8.08e+01 ... (remaining 94945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23713 17.68 - 35.37: 1898 35.37 - 53.05: 555 53.05 - 70.74: 147 70.74 - 88.42: 36 Dihedral angle restraints: 26349 sinusoidal: 14709 harmonic: 11640 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.37 61.63 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.43 61.57 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.59 61.41 1 1.00e+01 1.00e-02 5.01e+01 ... (remaining 26346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3740 0.072 - 0.144: 579 0.144 - 0.216: 88 0.216 - 0.287: 3 0.287 - 0.359: 3 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4410 not shown) Planarity restraints: 8004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB BLA B1815 " 0.052 2.00e-02 2.50e+03 6.17e-02 9.51e+01 pdb=" OB BLA B1815 " -0.006 2.00e-02 2.50e+03 pdb=" C1B BLA B1815 " 0.059 2.00e-02 2.50e+03 pdb=" C2B BLA B1815 " 0.013 2.00e-02 2.50e+03 pdb=" C3B BLA B1815 " -0.016 2.00e-02 2.50e+03 pdb=" C4A BLA B1815 " -0.139 2.00e-02 2.50e+03 pdb=" C4B BLA B1815 " 0.009 2.00e-02 2.50e+03 pdb=" CAB BLA B1815 " -0.064 2.00e-02 2.50e+03 pdb=" CHB BLA B1815 " 0.089 2.00e-02 2.50e+03 pdb=" CMB BLA B1815 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A1314 " 0.052 2.00e-02 2.50e+03 6.17e-02 9.51e+01 pdb=" OB BLA A1314 " -0.006 2.00e-02 2.50e+03 pdb=" C1B BLA A1314 " 0.059 2.00e-02 2.50e+03 pdb=" C2B BLA A1314 " 0.013 2.00e-02 2.50e+03 pdb=" C3B BLA A1314 " -0.015 2.00e-02 2.50e+03 pdb=" C4A BLA A1314 " -0.139 2.00e-02 2.50e+03 pdb=" C4B BLA A1314 " 0.009 2.00e-02 2.50e+03 pdb=" CAB BLA A1314 " -0.064 2.00e-02 2.50e+03 pdb=" CHB BLA A1314 " 0.089 2.00e-02 2.50e+03 pdb=" CMB BLA A1314 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA C1314 " -0.053 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" OB BLA C1314 " 0.006 2.00e-02 2.50e+03 pdb=" C1B BLA C1314 " -0.058 2.00e-02 2.50e+03 pdb=" C2B BLA C1314 " -0.012 2.00e-02 2.50e+03 pdb=" C3B BLA C1314 " 0.015 2.00e-02 2.50e+03 pdb=" C4A BLA C1314 " 0.139 2.00e-02 2.50e+03 pdb=" C4B BLA C1314 " -0.009 2.00e-02 2.50e+03 pdb=" CAB BLA C1314 " 0.064 2.00e-02 2.50e+03 pdb=" CHB BLA C1314 " -0.089 2.00e-02 2.50e+03 pdb=" CMB BLA C1314 " -0.003 2.00e-02 2.50e+03 ... (remaining 8001 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 4094 2.22 - 2.82: 109233 2.82 - 3.41: 136763 3.41 - 4.01: 192148 4.01 - 4.60: 292035 Nonbonded interactions: 734273 Sorted by model distance: nonbonded pdb=" O ALA B 879 " pdb=" HG1 THR B 883 " model vdw 1.626 1.850 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.646 1.850 nonbonded pdb=" HH TYR A 37 " pdb=" O LEU A 54 " model vdw 1.647 1.850 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.649 1.850 nonbonded pdb=" OG SER B1051 " pdb=" HD1 HIS B1064 " model vdw 1.651 1.850 ... (remaining 734268 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 14 through 1140 or resid 1302 through 1313)) selection = (chain 'B' and (resid 14 through 1140 or resid 1802 through 1813)) selection = (chain 'C' and (resid 14 through 1140 or resid 1302 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.570 Extract box with map and model: 10.560 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 124.800 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.162 27672 Z= 0.815 Angle : 1.016 32.167 37656 Z= 0.464 Chirality : 0.053 0.359 4413 Planarity : 0.005 0.062 4791 Dihedral : 14.239 88.420 10941 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.31 % Allowed : 0.80 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3312 helix: 0.15 (0.18), residues: 765 sheet: -0.15 (0.18), residues: 750 loop : -1.68 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.006 0.001 HIS A1048 PHE 0.047 0.002 PHE C 392 TYR 0.023 0.002 TYR B 365 ARG 0.008 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8149 (tp-100) REVERT: C 153 MET cc_start: 0.8150 (ppp) cc_final: 0.7927 (ppp) outliers start: 9 outliers final: 5 residues processed: 168 average time/residue: 0.7246 time to fit residues: 193.5068 Evaluate side-chains 113 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.6980 chunk 252 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 134 optimal weight: 0.0050 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 302 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27672 Z= 0.167 Angle : 0.553 14.156 37656 Z= 0.285 Chirality : 0.044 0.327 4413 Planarity : 0.004 0.051 4791 Dihedral : 8.252 59.728 5040 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.48 % Allowed : 3.39 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3312 helix: 0.45 (0.19), residues: 759 sheet: 0.01 (0.18), residues: 744 loop : -1.50 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS B 66 PHE 0.014 0.001 PHE C 392 TYR 0.014 0.001 TYR B 365 ARG 0.002 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8076 (mt0) REVERT: C 725 GLU cc_start: 0.8074 (pp20) cc_final: 0.7738 (pp20) outliers start: 14 outliers final: 7 residues processed: 135 average time/residue: 0.6794 time to fit residues: 150.0696 Evaluate side-chains 111 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain B residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 302 optimal weight: 0.4980 chunk 327 optimal weight: 0.0970 chunk 269 optimal weight: 0.6980 chunk 300 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 14 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 27672 Z= 0.151 Angle : 0.531 13.921 37656 Z= 0.273 Chirality : 0.043 0.312 4413 Planarity : 0.003 0.046 4791 Dihedral : 7.338 56.910 5034 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.59 % Allowed : 4.50 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3312 helix: 0.71 (0.20), residues: 762 sheet: 0.10 (0.18), residues: 750 loop : -1.44 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 245 PHE 0.010 0.001 PHE C 392 TYR 0.014 0.001 TYR B 365 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8322 (tp-100) cc_final: 0.8108 (mt0) REVERT: C 725 GLU cc_start: 0.7964 (pp20) cc_final: 0.7739 (pp20) outliers start: 17 outliers final: 8 residues processed: 131 average time/residue: 0.7196 time to fit residues: 154.8862 Evaluate side-chains 118 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 27672 Z= 0.370 Angle : 0.573 14.565 37656 Z= 0.297 Chirality : 0.045 0.306 4413 Planarity : 0.004 0.046 4791 Dihedral : 7.018 59.214 5034 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.59 % Allowed : 6.50 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3312 helix: 0.55 (0.19), residues: 762 sheet: -0.00 (0.17), residues: 774 loop : -1.52 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 PHE 0.017 0.001 PHE C 392 TYR 0.020 0.001 TYR B 365 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.7922 (mtm) cc_final: 0.7662 (mtp) REVERT: B 661 GLU cc_start: 0.8171 (pp20) cc_final: 0.7934 (pp20) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.7427 time to fit residues: 148.0356 Evaluate side-chains 119 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 828 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 274 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 360 ASN B 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 27672 Z= 0.417 Angle : 0.600 14.995 37656 Z= 0.313 Chirality : 0.046 0.304 4413 Planarity : 0.004 0.042 4791 Dihedral : 6.874 58.458 5034 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 0.80 % Allowed : 8.16 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3312 helix: 0.30 (0.19), residues: 759 sheet: -0.08 (0.18), residues: 774 loop : -1.61 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 PHE 0.023 0.001 PHE A 392 TYR 0.020 0.001 TYR B 365 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8053 (mtm) cc_final: 0.7834 (mtp) outliers start: 23 outliers final: 15 residues processed: 133 average time/residue: 0.7388 time to fit residues: 157.8372 Evaluate side-chains 122 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27672 Z= 0.287 Angle : 0.563 14.373 37656 Z= 0.293 Chirality : 0.044 0.306 4413 Planarity : 0.004 0.043 4791 Dihedral : 6.655 58.692 5034 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.66 % Allowed : 8.78 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3312 helix: 0.47 (0.19), residues: 756 sheet: -0.12 (0.18), residues: 756 loop : -1.54 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS C 66 PHE 0.015 0.001 PHE C 392 TYR 0.016 0.001 TYR B 365 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 3.011 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.7000 time to fit residues: 148.7311 Evaluate side-chains 126 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 987 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 320 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27672 Z= 0.272 Angle : 0.547 14.220 37656 Z= 0.284 Chirality : 0.044 0.295 4413 Planarity : 0.004 0.041 4791 Dihedral : 6.488 63.949 5034 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.73 % Allowed : 9.27 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3312 helix: 0.54 (0.19), residues: 756 sheet: -0.11 (0.18), residues: 756 loop : -1.52 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 66 PHE 0.014 0.001 PHE C 392 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 135 average time/residue: 0.7182 time to fit residues: 160.5756 Evaluate side-chains 131 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 137 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27672 Z= 0.265 Angle : 0.541 14.112 37656 Z= 0.281 Chirality : 0.044 0.297 4413 Planarity : 0.004 0.042 4791 Dihedral : 6.306 69.577 5034 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.97 % Allowed : 9.27 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3312 helix: 0.57 (0.19), residues: 759 sheet: -0.11 (0.18), residues: 756 loop : -1.50 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 207 PHE 0.014 0.001 PHE C 392 TYR 0.015 0.001 TYR C 365 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 3.056 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 141 average time/residue: 0.6893 time to fit residues: 159.2941 Evaluate side-chains 135 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 130 optimal weight: 0.0170 chunk 234 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 282 optimal weight: 0.0570 chunk 298 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 137 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 27672 Z= 0.155 Angle : 0.509 13.618 37656 Z= 0.264 Chirality : 0.043 0.280 4413 Planarity : 0.003 0.042 4791 Dihedral : 5.966 73.779 5034 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.69 % Allowed : 9.51 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3312 helix: 0.82 (0.20), residues: 756 sheet: 0.05 (0.18), residues: 774 loop : -1.41 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE C 392 TYR 0.013 0.001 TYR C 365 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 0.6766 time to fit residues: 150.6831 Evaluate side-chains 129 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 219 optimal weight: 0.0770 chunk 331 optimal weight: 0.0010 chunk 305 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 204 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 137 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 27672 Z= 0.159 Angle : 0.500 13.316 37656 Z= 0.259 Chirality : 0.043 0.280 4413 Planarity : 0.003 0.048 4791 Dihedral : 5.692 72.844 5034 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.62 % Allowed : 9.65 % Favored : 89.73 % 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: -0.63 (0.14), residues: 3312 helix: 0.96 (0.20), residues: 759 sheet: 0.13 (0.18), residues: 774 loop : -1.32 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE C 392 TYR 0.013 0.001 TYR C 365 ARG 0.008 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.6848 time to fit residues: 155.4599 Evaluate side-chains 130 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 987 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain B residue 991 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 243 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 137 ASN C 901 GLN B 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081175 restraints weight = 145862.699| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.76 r_work: 0.2982 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 27672 Z= 0.149 Angle : 0.495 13.141 37656 Z= 0.256 Chirality : 0.043 0.262 4413 Planarity : 0.003 0.044 4791 Dihedral : 5.525 73.401 5034 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.59 % Allowed : 9.65 % Favored : 89.76 % 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: -0.49 (0.14), residues: 3312 helix: 1.06 (0.20), residues: 759 sheet: 0.21 (0.18), residues: 771 loop : -1.21 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.000 HIS A 207 PHE 0.009 0.001 PHE C 392 TYR 0.012 0.001 TYR A 365 ARG 0.002 0.000 ARG B1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7138.49 seconds wall clock time: 125 minutes 41.89 seconds (7541.89 seconds total)