Starting phenix.real_space_refine on Tue Mar 26 00:25:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/03_2024/7xu6_33460_trim_updated.pdb" } resolution = 2.9 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 123 5.16 5 C 16902 2.51 5 N 4350 2.21 5 O 5187 1.98 5 H 24902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51464 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 16818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16818 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 Chain: "C" Number of atoms: 16817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16817 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 Chain: "B" Number of atoms: 16818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16818 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 22.42, per 1000 atoms: 0.44 Number of scatterers: 51464 At special positions: 0 Unit cell: (136.869, 148.54, 163.394, 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 123 16.00 O 5187 8.00 N 4350 7.00 C 16902 6.00 H 24902 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.04 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=2.02 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 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.04 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=2.02 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 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.05 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=2.04 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=2.02 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 B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " 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: 40.97 Conformation dependent library (CDL) restraints added in 5.7 seconds 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 45 sheets defined 20.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.69 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 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 385 through 388 removed outlier: 4.211A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.919A 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 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.506A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 817 through 822 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 909 removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.708A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.468A 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 removed outlier: 3.655A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 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 385 through 388 removed outlier: 4.205A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.918A 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 631 through 634 No H-bonds generated for 'chain 'C' and resid 631 through 634' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.501A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 817 through 822 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 909 removed outlier: 3.669A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.722A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.479A 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 removed outlier: 3.653A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 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 385 through 388 removed outlier: 4.210A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.912A 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 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.509A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 817 through 822 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 909 removed outlier: 3.670A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.720A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.480A 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 removed outlier: 3.659A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.989A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.976A 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 241 removed outlier: 3.974A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.911A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.736A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= G, first strand: chain 'A' and resid 552 through 554 Processing sheet with id= H, first strand: chain 'A' and resid 691 through 696 removed outlier: 5.710A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= J, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.933A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= M, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= N, first strand: chain 'A' and resid 141 through 145 removed outlier: 5.878A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 565 through 567 Processing sheet with id= P, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.968A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.971A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 237 through 241 removed outlier: 3.965A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.894A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.737A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'C' and resid 552 through 554 Processing sheet with id= W, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.713A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= Y, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.952A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.198A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AB, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= AC, first strand: chain 'C' and resid 141 through 145 removed outlier: 5.879A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 565 through 567 Processing sheet with id= AE, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.990A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.975A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 237 through 241 removed outlier: 3.970A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.896A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.740A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'B' and resid 552 through 554 Processing sheet with id= AL, first strand: chain 'B' and resid 691 through 696 removed outlier: 5.713A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= AN, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.212A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AQ, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AR, first strand: chain 'B' and resid 141 through 145 removed outlier: 5.879A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 565 through 567 838 hydrogen bonds defined for protein. 2343 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: 21.41 Time building geometry restraints manager: 42.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 24893 1.02 - 1.24: 3242 1.24 - 1.45: 8686 1.45 - 1.66: 15087 1.66 - 1.88: 153 Bond restraints: 52061 Sorted by residual: bond pdb=" NB BLA C1314 " pdb=" C4B BLA C1314 " ideal model delta sigma weight residual 1.371 1.535 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" NB BLA A1314 " pdb=" C4B BLA A1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" NB BLA B1314 " pdb=" C4B BLA B1314 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.57e+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 6.56e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.536 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 52056 not shown) Histogram of bond angle deviations from ideal: 90.10 - 102.23: 40 102.23 - 114.37: 62881 114.37 - 126.50: 30019 126.50 - 138.64: 389 138.64 - 150.77: 2 Bond angle restraints: 93331 Sorted by residual: angle pdb=" CD GLN A 628 " pdb=" NE2 GLN A 628 " pdb="HE22 GLN A 628 " ideal model delta sigma weight residual 120.00 150.77 -30.77 3.00e+00 1.11e-01 1.05e+02 angle pdb="HE21 GLN A 628 " pdb=" NE2 GLN A 628 " pdb="HE22 GLN A 628 " ideal model delta sigma weight residual 120.00 90.10 29.90 3.00e+00 1.11e-01 9.94e+01 angle pdb="HE21 GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE22 GLN C 628 " ideal model delta sigma weight residual 120.00 95.43 24.57 3.00e+00 1.11e-01 6.71e+01 angle pdb=" CD GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE22 GLN C 628 " ideal model delta sigma weight residual 120.00 144.18 -24.18 3.00e+00 1.11e-01 6.49e+01 angle pdb=" CD GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE21 GLN C 628 " ideal model delta sigma weight residual 120.00 96.47 23.53 3.00e+00 1.11e-01 6.15e+01 ... (remaining 93326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 23129 17.74 - 35.49: 2028 35.49 - 53.23: 513 53.23 - 70.97: 177 70.97 - 88.72: 24 Dihedral angle restraints: 25871 sinusoidal: 14439 harmonic: 11432 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.24 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.26 -58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.38 -58.62 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 25868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3569 0.066 - 0.133: 652 0.133 - 0.199: 115 0.199 - 0.265: 5 0.265 - 0.332: 6 Chirality restraints: 4347 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 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+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 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4344 not shown) Planarity restraints: 7833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.67e+02 pdb=" C1D BLA A1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA A1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA A1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA A1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA A1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA A1314 " 0.134 2.00e-02 2.50e+03 pdb=" NC BLA A1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA A1314 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.67e+02 pdb=" C1D BLA B1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA B1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA B1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA B1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA B1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA B1314 " 0.133 2.00e-02 2.50e+03 pdb=" NC BLA B1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA B1314 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.66e+02 pdb=" C1D BLA C1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA C1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA C1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA C1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA C1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA C1314 " 0.134 2.00e-02 2.50e+03 pdb=" NC BLA C1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA C1314 " 0.011 2.00e-02 2.50e+03 ... (remaining 7830 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 5776 2.24 - 2.83: 111989 2.83 - 3.42: 130165 3.42 - 4.01: 185998 4.01 - 4.60: 281462 Nonbonded interactions: 715390 Sorted by model distance: nonbonded pdb=" OG SER B1051 " pdb=" HD1 HIS B1064 " model vdw 1.655 1.850 nonbonded pdb=" OG SER A1051 " pdb=" HD1 HIS A1064 " model vdw 1.657 1.850 nonbonded pdb=" OE1 GLN A1002 " pdb="HE22 GLN C1005 " model vdw 1.671 1.850 nonbonded pdb="HE22 GLN A1005 " pdb=" OE1 GLN B1002 " model vdw 1.671 1.850 nonbonded pdb=" OE1 GLN C1002 " pdb="HE22 GLN B1005 " model vdw 1.673 1.850 ... (remaining 715385 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 17 through 1063 or (resid 1064 and (name N or name CA or n \ ame C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or nam \ e NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or na \ me HE2)) or resid 1065 through 1140 or resid 1301 through 1314)) selection = (chain 'B' and (resid 17 through 1063 or (resid 1064 and (name N or name CA or n \ ame C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or nam \ e NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or na \ me HE2)) or resid 1065 through 1140 or resid 1301 through 1314)) 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.830 Extract box with map and model: 12.600 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 161.610 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 0.164 27159 Z= 0.791 Angle : 0.955 15.523 36963 Z= 0.455 Chirality : 0.055 0.332 4347 Planarity : 0.006 0.137 4689 Dihedral : 14.180 88.717 10740 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.74 % Allowed : 0.56 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.74 (0.14), residues: 3231 helix: 0.18 (0.20), residues: 711 sheet: -0.65 (0.19), residues: 687 loop : -1.97 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP A 64 HIS 0.008 0.001 HIS B 245 PHE 0.015 0.002 PHE B 140 TYR 0.068 0.002 TYR C 904 ARG 0.010 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0632 (mtt) cc_final: -0.0859 (mtt) REVERT: A 516 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 629 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6602 (pp) REVERT: C 140 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (p90) REVERT: B 144 TYR cc_start: 0.6954 (t80) cc_final: 0.6633 (t80) REVERT: B 245 HIS cc_start: 0.7399 (m-70) cc_final: 0.6955 (m90) REVERT: B 731 MET cc_start: 0.9054 (ptt) cc_final: 0.8795 (ptt) outliers start: 21 outliers final: 3 residues processed: 249 average time/residue: 2.3826 time to fit residues: 717.4520 Evaluate side-chains 174 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS C1005 GLN C1088 HIS B1005 GLN B1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27159 Z= 0.204 Angle : 0.580 10.571 36963 Z= 0.298 Chirality : 0.045 0.289 4347 Planarity : 0.003 0.041 4689 Dihedral : 8.609 59.592 4919 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.88 % Allowed : 5.37 % Favored : 93.75 % 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: -1.43 (0.14), residues: 3231 helix: 0.74 (0.21), residues: 693 sheet: -0.53 (0.18), residues: 666 loop : -1.84 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS A 519 PHE 0.011 0.001 PHE C 140 TYR 0.024 0.001 TYR B 904 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7855 (t0) cc_final: 0.7620 (t0) REVERT: A 516 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7067 (tm-30) REVERT: A 629 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6615 (pp) REVERT: C 140 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8343 (p90) REVERT: C 837 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: B 140 PHE cc_start: 0.8617 (p90) cc_final: 0.8210 (p90) REVERT: B 177 MET cc_start: -0.0346 (mtt) cc_final: -0.0726 (mtt) REVERT: B 228 ASP cc_start: 0.7986 (t0) cc_final: 0.7775 (t0) REVERT: B 245 HIS cc_start: 0.7359 (m-70) cc_final: 0.6934 (m90) REVERT: B 837 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.5778 (m-80) outliers start: 25 outliers final: 15 residues processed: 196 average time/residue: 2.0874 time to fit residues: 509.4788 Evaluate side-chains 191 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS B 628 GLN B 965 GLN B1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27159 Z= 0.281 Angle : 0.564 10.750 36963 Z= 0.293 Chirality : 0.044 0.281 4347 Planarity : 0.003 0.040 4689 Dihedral : 7.504 59.863 4919 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.16 % Allowed : 6.42 % Favored : 92.42 % 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: -1.32 (0.14), residues: 3231 helix: 0.74 (0.20), residues: 735 sheet: -0.54 (0.18), residues: 681 loop : -1.75 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B 245 PHE 0.017 0.001 PHE B 220 TYR 0.021 0.001 TYR B 904 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7890 (t0) cc_final: 0.7626 (t0) REVERT: A 516 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 837 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.5939 (m-80) REVERT: A 986 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7858 (ttpp) REVERT: C 140 PHE cc_start: 0.8801 (p90) cc_final: 0.8364 (p90) REVERT: C 837 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: B 140 PHE cc_start: 0.8648 (p90) cc_final: 0.8287 (p90) REVERT: B 177 MET cc_start: 0.0210 (mtt) cc_final: -0.0098 (mtt) REVERT: B 245 HIS cc_start: 0.7424 (m-70) cc_final: 0.6929 (m90) REVERT: B 731 MET cc_start: 0.9241 (ptt) cc_final: 0.9028 (ptt) REVERT: B 837 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.5704 (m-80) outliers start: 33 outliers final: 14 residues processed: 203 average time/residue: 2.0473 time to fit residues: 516.8369 Evaluate side-chains 189 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27159 Z= 0.289 Angle : 0.557 10.601 36963 Z= 0.290 Chirality : 0.044 0.285 4347 Planarity : 0.003 0.037 4689 Dihedral : 6.977 59.482 4915 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.12 % Allowed : 7.86 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3231 helix: 0.86 (0.20), residues: 738 sheet: -0.46 (0.18), residues: 681 loop : -1.70 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.013 0.001 PHE B 220 TYR 0.014 0.001 TYR B 265 ARG 0.002 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7955 (t0) cc_final: 0.7693 (t0) REVERT: A 516 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 837 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6012 (m-80) REVERT: A 986 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7554 (ttpp) REVERT: C 140 PHE cc_start: 0.8862 (p90) cc_final: 0.8418 (p90) REVERT: C 516 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: C 837 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: B 140 PHE cc_start: 0.8692 (p90) cc_final: 0.8480 (p90) REVERT: B 177 MET cc_start: 0.0393 (mtt) cc_final: 0.0123 (mtt) REVERT: B 245 HIS cc_start: 0.7375 (m-70) cc_final: 0.6882 (m90) REVERT: B 731 MET cc_start: 0.9288 (ptt) cc_final: 0.9072 (ptt) REVERT: B 837 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.5772 (m-80) outliers start: 32 outliers final: 18 residues processed: 199 average time/residue: 2.0701 time to fit residues: 515.7730 Evaluate side-chains 196 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 0.6980 chunk 79 optimal weight: 0.0040 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27159 Z= 0.194 Angle : 0.531 10.123 36963 Z= 0.274 Chirality : 0.043 0.284 4347 Planarity : 0.003 0.036 4689 Dihedral : 6.604 59.990 4915 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.98 % Allowed : 8.88 % Favored : 90.14 % 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: -1.10 (0.14), residues: 3231 helix: 1.00 (0.21), residues: 738 sheet: -0.45 (0.18), residues: 711 loop : -1.65 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 353 HIS 0.002 0.001 HIS C 245 PHE 0.012 0.001 PHE B 898 TYR 0.012 0.001 TYR C 265 ARG 0.001 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7918 (t0) cc_final: 0.7646 (t0) REVERT: A 516 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 837 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: A 934 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9091 (OUTLIER) REVERT: C 140 PHE cc_start: 0.8859 (p90) cc_final: 0.8436 (p90) REVERT: C 516 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: C 837 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: B 177 MET cc_start: 0.0148 (mtt) cc_final: -0.0097 (mtt) REVERT: B 245 HIS cc_start: 0.7329 (m-70) cc_final: 0.6833 (m90) REVERT: B 837 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.5773 (m-80) outliers start: 28 outliers final: 13 residues processed: 193 average time/residue: 2.0680 time to fit residues: 508.1233 Evaluate side-chains 187 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 145 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27159 Z= 0.263 Angle : 0.538 10.260 36963 Z= 0.279 Chirality : 0.044 0.285 4347 Planarity : 0.003 0.035 4689 Dihedral : 6.255 59.689 4914 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.30 % Allowed : 9.23 % 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: -1.09 (0.14), residues: 3231 helix: 1.02 (0.20), residues: 738 sheet: -0.42 (0.18), residues: 711 loop : -1.67 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.003 0.001 HIS B 245 PHE 0.012 0.001 PHE C 898 TYR 0.013 0.001 TYR A 508 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7926 (t0) cc_final: 0.7658 (t0) REVERT: A 516 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 837 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6044 (m-80) REVERT: C 140 PHE cc_start: 0.8887 (p90) cc_final: 0.8457 (p90) REVERT: C 837 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: B 177 MET cc_start: 0.0266 (mtt) cc_final: 0.0050 (mtt) REVERT: B 837 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.5623 (m-80) outliers start: 37 outliers final: 18 residues processed: 204 average time/residue: 1.9901 time to fit residues: 508.3921 Evaluate side-chains 193 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 312 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27159 Z= 0.217 Angle : 0.526 9.870 36963 Z= 0.272 Chirality : 0.043 0.283 4347 Planarity : 0.003 0.036 4689 Dihedral : 6.058 59.961 4913 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.12 % Allowed : 10.00 % Favored : 88.88 % 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: 3231 helix: 1.12 (0.20), residues: 735 sheet: -0.38 (0.18), residues: 711 loop : -1.62 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.004 0.001 HIS B 245 PHE 0.012 0.001 PHE C 220 TYR 0.014 0.001 TYR A 508 ARG 0.001 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7826 (t0) cc_final: 0.7539 (t0) REVERT: A 516 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 837 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.5971 (m-80) REVERT: C 140 PHE cc_start: 0.8870 (p90) cc_final: 0.8472 (p90) REVERT: C 837 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: B 177 MET cc_start: 0.0311 (mtt) cc_final: 0.0099 (mtt) REVERT: B 837 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.5661 (m-80) outliers start: 32 outliers final: 13 residues processed: 199 average time/residue: 1.9993 time to fit residues: 498.7876 Evaluate side-chains 190 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27159 Z= 0.290 Angle : 0.546 10.217 36963 Z= 0.283 Chirality : 0.044 0.287 4347 Planarity : 0.003 0.035 4689 Dihedral : 5.946 59.141 4913 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.95 % Allowed : 10.42 % Favored : 88.63 % 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: -1.05 (0.14), residues: 3231 helix: 1.06 (0.20), residues: 738 sheet: -0.42 (0.18), residues: 696 loop : -1.63 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.013 0.001 PHE C 220 TYR 0.018 0.001 TYR A 508 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7960 (t0) cc_final: 0.7682 (t0) REVERT: A 516 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7084 (tm-30) REVERT: A 837 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: C 140 PHE cc_start: 0.8895 (p90) cc_final: 0.8517 (p90) REVERT: C 837 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: B 837 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.5704 (m-80) outliers start: 27 outliers final: 14 residues processed: 197 average time/residue: 1.9242 time to fit residues: 474.3182 Evaluate side-chains 192 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.5980 chunk 299 optimal weight: 0.9990 chunk 272 optimal weight: 0.5980 chunk 291 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 0.0770 chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27159 Z= 0.158 Angle : 0.514 9.278 36963 Z= 0.265 Chirality : 0.043 0.284 4347 Planarity : 0.003 0.036 4689 Dihedral : 5.734 57.320 4913 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.70 % Allowed : 10.77 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3231 helix: 1.25 (0.21), residues: 735 sheet: -0.29 (0.18), residues: 696 loop : -1.53 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS C 625 PHE 0.012 0.001 PHE A 220 TYR 0.014 0.001 TYR A 508 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7927 (t0) cc_final: 0.7632 (t0) REVERT: A 516 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 837 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: A 1050 MET cc_start: 0.8848 (ptp) cc_final: 0.8233 (ptp) REVERT: C 140 PHE cc_start: 0.8873 (p90) cc_final: 0.8444 (p90) REVERT: C 837 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: B 837 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.5614 (m-80) outliers start: 20 outliers final: 11 residues processed: 196 average time/residue: 1.9845 time to fit residues: 487.3480 Evaluate side-chains 186 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 297 optimal weight: 0.0980 chunk 257 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27159 Z= 0.174 Angle : 0.509 9.178 36963 Z= 0.263 Chirality : 0.043 0.281 4347 Planarity : 0.003 0.036 4689 Dihedral : 5.522 56.207 4913 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.74 % Allowed : 11.09 % Favored : 88.18 % 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: -0.80 (0.15), residues: 3231 helix: 1.30 (0.20), residues: 735 sheet: -0.24 (0.18), residues: 696 loop : -1.49 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.000 HIS C 245 PHE 0.013 0.001 PHE C 220 TYR 0.014 0.001 TYR C 508 ARG 0.003 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7926 (t0) cc_final: 0.7626 (t0) REVERT: A 516 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 837 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: C 140 PHE cc_start: 0.8869 (p90) cc_final: 0.8436 (p90) REVERT: C 837 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: B 837 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.5655 (m-80) outliers start: 21 outliers final: 12 residues processed: 193 average time/residue: 1.9123 time to fit residues: 459.9866 Evaluate side-chains 186 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 0.0000 chunk 107 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 957 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091941 restraints weight = 139224.633| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.10 r_work: 0.3160 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27159 Z= 0.197 Angle : 0.512 9.151 36963 Z= 0.264 Chirality : 0.043 0.279 4347 Planarity : 0.003 0.036 4689 Dihedral : 5.437 57.515 4913 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.63 % Allowed : 11.44 % Favored : 87.93 % 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: -0.79 (0.15), residues: 3231 helix: 1.32 (0.20), residues: 735 sheet: -0.25 (0.18), residues: 711 loop : -1.49 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE A 220 TYR 0.014 0.001 TYR C 508 ARG 0.002 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12171.65 seconds wall clock time: 214 minutes 38.82 seconds (12878.82 seconds total)