Starting phenix.real_space_refine on Wed Feb 21 07:42:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cim_16678/02_2024/8cim_16678.pdb" } resolution = 3.0 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19026 2.51 5 N 4938 2.21 5 O 5835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29928 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "B" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "C" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "D" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "S" 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: "T" 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: "U" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.63, per 1000 atoms: 0.52 Number of scatterers: 29928 At special positions: 0 Unit cell: (135.106, 140.218, 187.687, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5835 8.00 N 4938 7.00 C 19026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 328 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 600 " " NAG B1304 " - " ASN B 613 " " NAG B1305 " - " ASN B 654 " " NAG B1306 " - " ASN B 706 " " NAG B1307 " - " ASN B1071 " " NAG B1308 " - " ASN B 328 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 11.88 Conformation dependent library (CDL) restraints added in 5.6 seconds 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6990 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 60 sheets defined 22.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.571A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.575A pdb=" N PHE A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.668A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.994A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.647A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.531A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.094A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.210A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.055A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.581A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.575A pdb=" N PHE B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.657A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.001A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.652A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.523A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.078A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.191A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.052A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.579A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.574A pdb=" N PHE C 368 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.666A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.997A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.651A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.514A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.090A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.198A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.056A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.790A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.110A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.126A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.616A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.614A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.935A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.893A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.746A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.178A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 562 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.693A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.275A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 712 removed outlier: 3.813A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.970A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.555A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.795A pdb=" N ILE A 785 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.528A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.615A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.648A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.917A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.902A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.757A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.688A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.277A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.826A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.993A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.550A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.819A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.530A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.615A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 226 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.900A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.895A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.755A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE2, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.696A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.259A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 712 removed outlier: 3.807A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.979A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.575A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.528A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.390A pdb=" N GLU D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.390A pdb=" N GLU D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 98 " --> pdb=" O PRO D 115 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.730A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.821A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 98 " --> pdb=" O PRO F 115 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.743A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.825A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG H 98 " --> pdb=" O PRO H 115 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.705A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1233 hydrogen bonds defined for protein. 3261 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: 16.33 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9522 1.34 - 1.46: 7104 1.46 - 1.58: 13800 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 30588 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 30583 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 816 106.52 - 113.39: 16846 113.39 - 120.27: 10343 120.27 - 127.14: 13277 127.14 - 134.01: 280 Bond angle restraints: 41562 Sorted by residual: angle pdb=" N GLY A1090 " pdb=" CA GLY A1090 " pdb=" C GLY A1090 " ideal model delta sigma weight residual 110.43 114.43 -4.00 1.35e+00 5.49e-01 8.78e+00 angle pdb=" N GLY C1090 " pdb=" CA GLY C1090 " pdb=" C GLY C1090 " ideal model delta sigma weight residual 110.43 114.38 -3.95 1.35e+00 5.49e-01 8.54e+00 angle pdb=" N GLY B1090 " pdb=" CA GLY B1090 " pdb=" C GLY B1090 " ideal model delta sigma weight residual 110.43 114.37 -3.94 1.35e+00 5.49e-01 8.50e+00 angle pdb=" C THR C 312 " pdb=" N SER C 313 " pdb=" CA SER C 313 " ideal model delta sigma weight residual 122.20 117.37 4.83 1.72e+00 3.38e-01 7.88e+00 angle pdb=" C THR B 312 " pdb=" N SER B 313 " pdb=" CA SER B 313 " ideal model delta sigma weight residual 122.39 117.85 4.54 1.64e+00 3.72e-01 7.67e+00 ... (remaining 41557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17881 18.00 - 35.99: 751 35.99 - 53.99: 132 53.99 - 71.99: 22 71.99 - 89.98: 9 Dihedral angle restraints: 18795 sinusoidal: 7902 harmonic: 10893 Sorted by residual: dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 18792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4199 0.067 - 0.133: 598 0.133 - 0.200: 30 0.200 - 0.266: 0 0.266 - 0.333: 3 Chirality restraints: 4830 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 600 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 600 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 600 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4827 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 13 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO H 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 13 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO F 14 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 13 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO D 14 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.020 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1702 2.73 - 3.27: 28062 3.27 - 3.81: 47356 3.81 - 4.36: 59248 4.36 - 4.90: 104710 Nonbonded interactions: 241078 Sorted by model distance: nonbonded pdb=" N ASP D 114 " pdb=" OD1 ASP D 114 " model vdw 2.186 2.520 nonbonded pdb=" N ASP F 114 " pdb=" OD1 ASP F 114 " model vdw 2.190 2.520 nonbonded pdb=" N ASP H 114 " pdb=" OD1 ASP H 114 " model vdw 2.201 2.520 nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.236 2.440 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.239 2.440 ... (remaining 241073 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 12.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 43.070 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 84.840 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.004 0.052 30588 Z= 0.278 Angle : 0.540 7.631 41562 Z= 0.274 Chirality : 0.046 0.333 4830 Planarity : 0.004 0.037 5295 Dihedral : 10.290 89.984 11670 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.95 % Allowed : 3.78 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3699 helix: 1.90 (0.20), residues: 684 sheet: 0.14 (0.17), residues: 963 loop : -0.70 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 433 HIS 0.004 0.001 HIS C1061 PHE 0.014 0.001 PHE B 374 TYR 0.018 0.001 TYR A 492 ARG 0.003 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 495 time to evaluate : 3.503 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 26 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.7033 (p) REVERT: A 87 VAL cc_start: 0.8858 (t) cc_final: 0.8569 (p) REVERT: A 302 SER cc_start: 0.9045 (t) cc_final: 0.8830 (p) REVERT: A 311 GLN cc_start: 0.7719 (tt0) cc_final: 0.7485 (tp-100) REVERT: A 336 ASP cc_start: 0.7947 (m-30) cc_final: 0.7681 (m-30) REVERT: A 340 ASN cc_start: 0.7722 (t0) cc_final: 0.7456 (p0) REVERT: A 354 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7985 (ttp80) REVERT: A 513 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6289 (tt0) REVERT: A 526 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7632 (mptt) REVERT: A 1014 GLU cc_start: 0.8405 (tt0) cc_final: 0.8159 (tt0) REVERT: B 26 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6186 (p) REVERT: B 81 LEU cc_start: 0.6909 (mm) cc_final: 0.6682 (mp) REVERT: B 87 VAL cc_start: 0.8716 (t) cc_final: 0.8313 (p) REVERT: B 302 SER cc_start: 0.9068 (t) cc_final: 0.8579 (p) REVERT: B 311 GLN cc_start: 0.7588 (tt0) cc_final: 0.7097 (tp-100) REVERT: B 322 SER cc_start: 0.8792 (p) cc_final: 0.8592 (p) REVERT: B 336 ASP cc_start: 0.7937 (m-30) cc_final: 0.7497 (m-30) REVERT: B 340 ASN cc_start: 0.7707 (t0) cc_final: 0.7020 (p0) REVERT: B 354 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7915 (ttp80) REVERT: B 526 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7315 (mptt) REVERT: B 773 LYS cc_start: 0.8098 (tttt) cc_final: 0.7708 (tttm) REVERT: B 777 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7745 (mm-30) REVERT: B 947 ASP cc_start: 0.7510 (m-30) cc_final: 0.7265 (OUTLIER) REVERT: B 1014 GLU cc_start: 0.7920 (tt0) cc_final: 0.7578 (tt0) REVERT: B 1042 LYS cc_start: 0.8388 (mttt) cc_final: 0.8177 (mptt) REVERT: B 1111 ILE cc_start: 0.8196 (mm) cc_final: 0.7876 (tp) REVERT: B 1135 TYR cc_start: 0.7493 (t80) cc_final: 0.7203 (t80) REVERT: C 26 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6839 (p) REVERT: C 81 LEU cc_start: 0.7252 (mm) cc_final: 0.7022 (mp) REVERT: C 87 VAL cc_start: 0.8889 (t) cc_final: 0.8541 (p) REVERT: C 197 TYR cc_start: 0.6997 (m-80) cc_final: 0.6586 (m-10) REVERT: C 302 SER cc_start: 0.9051 (t) cc_final: 0.8777 (p) REVERT: C 311 GLN cc_start: 0.7631 (tt0) cc_final: 0.7380 (tp-100) REVERT: C 336 ASP cc_start: 0.7979 (m-30) cc_final: 0.7684 (m-30) REVERT: C 340 ASN cc_start: 0.7727 (t0) cc_final: 0.7326 (p0) REVERT: C 354 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7970 (ttp80) REVERT: C 526 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7585 (mptt) REVERT: C 1014 GLU cc_start: 0.8359 (tt0) cc_final: 0.8074 (tt0) REVERT: C 1135 TYR cc_start: 0.7679 (t80) cc_final: 0.7396 (t80) REVERT: D 81 MET cc_start: 0.6939 (ttp) cc_final: 0.6592 (ttp) REVERT: H 64 PHE cc_start: 0.5923 (m-80) cc_final: 0.5583 (m-10) outliers start: 31 outliers final: 15 residues processed: 522 average time/residue: 1.2718 time to fit residues: 793.5820 Evaluate side-chains 294 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 277 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 0.0570 chunk 291 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 8.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 898 GLN B 84 ASN B 414 ASN B 801 GLN C 471 GLN C 604 GLN C 801 GLN C 898 GLN D 101 HIS E 37 GLN F 39 GLN F 100 GLN G 37 GLN G 38 GLN L 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30588 Z= 0.204 Angle : 0.526 9.670 41562 Z= 0.272 Chirality : 0.044 0.237 4830 Planarity : 0.004 0.050 5295 Dihedral : 6.284 123.859 5063 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.30 % Allowed : 10.23 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.11 (0.14), residues: 3699 helix: 2.00 (0.20), residues: 687 sheet: 0.09 (0.16), residues: 1005 loop : -0.59 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 36 HIS 0.005 0.001 HIS E 55 PHE 0.013 0.001 PHE E 71 TYR 0.017 0.001 TYR E 36 ARG 0.005 0.000 ARG C 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 289 time to evaluate : 3.743 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: A 26 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6899 (p) REVERT: A 50 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7720 (t70) REVERT: A 87 VAL cc_start: 0.8828 (t) cc_final: 0.8546 (p) REVERT: A 336 ASP cc_start: 0.7852 (m-30) cc_final: 0.7519 (m-30) REVERT: A 340 ASN cc_start: 0.7476 (t0) cc_final: 0.7117 (p0) REVERT: A 354 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7913 (ttp80) REVERT: A 513 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6256 (tt0) REVERT: A 526 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7605 (mptt) REVERT: A 1014 GLU cc_start: 0.8402 (tt0) cc_final: 0.8156 (tt0) REVERT: B 26 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.6130 (p) REVERT: B 50 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7393 (t70) REVERT: B 81 LEU cc_start: 0.6958 (mm) cc_final: 0.6661 (mp) REVERT: B 87 VAL cc_start: 0.8721 (t) cc_final: 0.8326 (p) REVERT: B 295 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: B 302 SER cc_start: 0.9114 (t) cc_final: 0.8660 (p) REVERT: B 311 GLN cc_start: 0.7494 (tt0) cc_final: 0.6977 (tp-100) REVERT: B 336 ASP cc_start: 0.7713 (m-30) cc_final: 0.7195 (m-30) REVERT: B 340 ASN cc_start: 0.7517 (t0) cc_final: 0.6731 (p0) REVERT: B 354 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7876 (ttp80) REVERT: B 526 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7328 (mptt) REVERT: B 773 LYS cc_start: 0.8078 (tttt) cc_final: 0.7726 (tttm) REVERT: B 777 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7660 (mm-30) REVERT: B 897 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: B 947 ASP cc_start: 0.7464 (m-30) cc_final: 0.7180 (t0) REVERT: B 1014 GLU cc_start: 0.7959 (tt0) cc_final: 0.7640 (tt0) REVERT: B 1042 LYS cc_start: 0.8339 (mttt) cc_final: 0.8071 (mptt) REVERT: B 1111 ILE cc_start: 0.8204 (mm) cc_final: 0.7958 (tp) REVERT: B 1122 ASN cc_start: 0.8201 (p0) cc_final: 0.7998 (p0) REVERT: B 1135 TYR cc_start: 0.7506 (t80) cc_final: 0.7209 (t80) REVERT: C 26 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6739 (p) REVERT: C 50 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7489 (t70) REVERT: C 81 LEU cc_start: 0.7386 (mm) cc_final: 0.7105 (mp) REVERT: C 87 VAL cc_start: 0.8883 (t) cc_final: 0.8541 (p) REVERT: C 197 TYR cc_start: 0.7026 (m-80) cc_final: 0.6640 (m-80) REVERT: C 302 SER cc_start: 0.9099 (t) cc_final: 0.8845 (p) REVERT: C 311 GLN cc_start: 0.7540 (tt0) cc_final: 0.7307 (tp-100) REVERT: C 336 ASP cc_start: 0.7852 (m-30) cc_final: 0.7464 (m-30) REVERT: C 340 ASN cc_start: 0.7446 (t0) cc_final: 0.6997 (p0) REVERT: C 354 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7937 (ttp80) REVERT: C 526 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7629 (mptt) REVERT: C 571 ASP cc_start: 0.7522 (t0) cc_final: 0.7261 (t0) REVERT: C 1014 GLU cc_start: 0.8358 (tt0) cc_final: 0.8006 (tt0) REVERT: C 1135 TYR cc_start: 0.7671 (t80) cc_final: 0.7419 (t80) REVERT: H 64 PHE cc_start: 0.5871 (m-80) cc_final: 0.5555 (m-10) outliers start: 75 outliers final: 41 residues processed: 344 average time/residue: 1.0999 time to fit residues: 469.0985 Evaluate side-chains 309 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 chunk 365 optimal weight: 40.0000 chunk 301 optimal weight: 0.6980 chunk 335 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN B 131 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 850 GLN B 898 GLN B 932 GLN C 131 GLN C 516 HIS C 962 GLN D 101 HIS F 39 GLN L 92 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30588 Z= 0.386 Angle : 0.591 9.234 41562 Z= 0.305 Chirality : 0.047 0.238 4830 Planarity : 0.004 0.057 5295 Dihedral : 5.810 51.513 5056 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.47 % Allowed : 10.97 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.12 (0.14), residues: 3699 helix: 1.80 (0.20), residues: 666 sheet: 0.16 (0.16), residues: 987 loop : -0.84 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 35 HIS 0.005 0.001 HIS C1061 PHE 0.018 0.002 PHE B 426 TYR 0.019 0.002 TYR B1064 ARG 0.004 0.001 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 284 time to evaluate : 3.736 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: A 26 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6931 (p) REVERT: A 50 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8024 (t70) REVERT: A 87 VAL cc_start: 0.8863 (t) cc_final: 0.8583 (p) REVERT: A 197 TYR cc_start: 0.7134 (m-80) cc_final: 0.6880 (m-80) REVERT: A 336 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: A 340 ASN cc_start: 0.7578 (t0) cc_final: 0.7155 (p0) REVERT: A 354 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7881 (ttp80) REVERT: A 513 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6337 (tt0) REVERT: A 526 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7688 (mptt) REVERT: A 1014 GLU cc_start: 0.8530 (tt0) cc_final: 0.8270 (tt0) REVERT: B 26 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6091 (p) REVERT: B 81 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6616 (mp) REVERT: B 87 VAL cc_start: 0.8727 (t) cc_final: 0.8345 (p) REVERT: B 295 GLU cc_start: 0.7581 (tt0) cc_final: 0.7196 (tp30) REVERT: B 302 SER cc_start: 0.9124 (t) cc_final: 0.8644 (p) REVERT: B 311 GLN cc_start: 0.7546 (tt0) cc_final: 0.7036 (tp-100) REVERT: B 336 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: B 340 ASN cc_start: 0.7554 (t0) cc_final: 0.6732 (p0) REVERT: B 354 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7854 (ttp80) REVERT: B 526 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7447 (mptt) REVERT: B 534 LYS cc_start: 0.8019 (mttt) cc_final: 0.7586 (mtpp) REVERT: B 773 LYS cc_start: 0.8161 (tttt) cc_final: 0.7763 (tttm) REVERT: B 777 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7686 (mm-30) REVERT: B 851 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7476 (tttm) REVERT: B 947 ASP cc_start: 0.7612 (m-30) cc_final: 0.7290 (t0) REVERT: B 995 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 1014 GLU cc_start: 0.8067 (tt0) cc_final: 0.7701 (tt0) REVERT: B 1042 LYS cc_start: 0.8330 (mttt) cc_final: 0.7994 (mptt) REVERT: B 1111 ILE cc_start: 0.8160 (mm) cc_final: 0.7930 (tp) REVERT: B 1135 TYR cc_start: 0.7503 (t80) cc_final: 0.7191 (t80) REVERT: C 26 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6772 (p) REVERT: C 87 VAL cc_start: 0.8933 (t) cc_final: 0.8572 (p) REVERT: C 197 TYR cc_start: 0.7106 (m-80) cc_final: 0.6619 (m-10) REVERT: C 266 TYR cc_start: 0.8627 (m-80) cc_final: 0.8363 (m-10) REVERT: C 302 SER cc_start: 0.9107 (t) cc_final: 0.8794 (m) REVERT: C 311 GLN cc_start: 0.7568 (tt0) cc_final: 0.7310 (tp-100) REVERT: C 336 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: C 340 ASN cc_start: 0.7538 (t0) cc_final: 0.6956 (p0) REVERT: C 354 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7862 (ttp80) REVERT: C 526 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7674 (mptt) REVERT: C 534 LYS cc_start: 0.8227 (mttt) cc_final: 0.8022 (mtpp) REVERT: C 571 ASP cc_start: 0.7758 (t0) cc_final: 0.7518 (t0) REVERT: C 672 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: C 974 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 1014 GLU cc_start: 0.8448 (tt0) cc_final: 0.8064 (tt0) REVERT: C 1135 TYR cc_start: 0.7742 (t80) cc_final: 0.7497 (t80) REVERT: F 81 MET cc_start: 0.7773 (ttp) cc_final: 0.7342 (ttp) REVERT: H 64 PHE cc_start: 0.5859 (m-80) cc_final: 0.5555 (m-10) outliers start: 113 outliers final: 57 residues processed: 371 average time/residue: 1.0634 time to fit residues: 490.0444 Evaluate side-chains 333 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 932 GLN Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.0040 chunk 254 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 0.0970 chunk 227 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 359 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 932 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30588 Z= 0.180 Angle : 0.502 9.842 41562 Z= 0.258 Chirality : 0.044 0.205 4830 Planarity : 0.004 0.050 5295 Dihedral : 5.287 52.052 5056 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.86 % Allowed : 12.87 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.12 (0.14), residues: 3699 helix: 2.13 (0.21), residues: 666 sheet: 0.36 (0.17), residues: 933 loop : -0.74 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 35 HIS 0.003 0.000 HIS C 204 PHE 0.018 0.001 PHE F 29 TYR 0.016 0.001 TYR A1064 ARG 0.003 0.000 ARG C 992 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 281 time to evaluate : 4.025 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 26 THR cc_start: 0.7080 (OUTLIER) cc_final: 0.6859 (p) REVERT: A 87 VAL cc_start: 0.8813 (t) cc_final: 0.8530 (p) REVERT: A 336 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: A 340 ASN cc_start: 0.7559 (t0) cc_final: 0.7070 (p0) REVERT: A 354 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7856 (ttp80) REVERT: A 513 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6215 (tt0) REVERT: A 526 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7688 (mptt) REVERT: A 1014 GLU cc_start: 0.8426 (tt0) cc_final: 0.8174 (tt0) REVERT: B 26 THR cc_start: 0.6433 (OUTLIER) cc_final: 0.5998 (p) REVERT: B 27 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7645 (t0) REVERT: B 81 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6591 (mp) REVERT: B 87 VAL cc_start: 0.8716 (t) cc_final: 0.8303 (p) REVERT: B 295 GLU cc_start: 0.7541 (tt0) cc_final: 0.7161 (tp30) REVERT: B 302 SER cc_start: 0.9118 (t) cc_final: 0.8682 (p) REVERT: B 311 GLN cc_start: 0.7393 (tt0) cc_final: 0.6954 (tp-100) REVERT: B 336 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: B 340 ASN cc_start: 0.7463 (t0) cc_final: 0.6668 (p0) REVERT: B 354 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7826 (ttp80) REVERT: B 475 LYS cc_start: 0.7429 (mmtt) cc_final: 0.7181 (pttt) REVERT: B 526 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7471 (mptt) REVERT: B 773 LYS cc_start: 0.8104 (tttt) cc_final: 0.7749 (tttm) REVERT: B 776 GLN cc_start: 0.7767 (tp40) cc_final: 0.7275 (tp40) REVERT: B 777 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7592 (mm-30) REVERT: B 851 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7409 (tttm) REVERT: B 897 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: B 947 ASP cc_start: 0.7505 (m-30) cc_final: 0.7166 (t0) REVERT: B 1014 GLU cc_start: 0.7982 (tt0) cc_final: 0.7662 (tt0) REVERT: B 1042 LYS cc_start: 0.8299 (mttt) cc_final: 0.8012 (mptt) REVERT: B 1111 ILE cc_start: 0.8188 (mm) cc_final: 0.7968 (tp) REVERT: B 1122 ASN cc_start: 0.8074 (p0) cc_final: 0.7839 (p0) REVERT: B 1135 TYR cc_start: 0.7474 (t80) cc_final: 0.7161 (t80) REVERT: C 26 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6736 (p) REVERT: C 81 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7045 (mp) REVERT: C 87 VAL cc_start: 0.8898 (t) cc_final: 0.8535 (p) REVERT: C 197 TYR cc_start: 0.7066 (m-80) cc_final: 0.6564 (m-10) REVERT: C 266 TYR cc_start: 0.8607 (m-80) cc_final: 0.8342 (m-10) REVERT: C 302 SER cc_start: 0.9092 (t) cc_final: 0.8792 (m) REVERT: C 311 GLN cc_start: 0.7482 (tt0) cc_final: 0.7251 (tp-100) REVERT: C 336 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: C 340 ASN cc_start: 0.7439 (t0) cc_final: 0.6825 (p0) REVERT: C 354 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7858 (ttp80) REVERT: C 526 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7669 (mptt) REVERT: C 571 ASP cc_start: 0.7724 (t0) cc_final: 0.7496 (t0) REVERT: C 672 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7363 (mt0) REVERT: C 1014 GLU cc_start: 0.8365 (tt0) cc_final: 0.8018 (tt0) REVERT: C 1135 TYR cc_start: 0.7707 (t80) cc_final: 0.7471 (t80) REVERT: F 81 MET cc_start: 0.7773 (ttp) cc_final: 0.7391 (ttp) REVERT: H 64 PHE cc_start: 0.5733 (m-80) cc_final: 0.5478 (m-10) outliers start: 93 outliers final: 43 residues processed: 351 average time/residue: 1.0861 time to fit residues: 469.1707 Evaluate side-chains 316 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 322 optimal weight: 0.0870 chunk 90 optimal weight: 0.6980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 932 GLN A1122 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 101 HIS E 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30588 Z= 0.220 Angle : 0.510 10.101 41562 Z= 0.261 Chirality : 0.044 0.209 4830 Planarity : 0.004 0.052 5295 Dihedral : 5.086 52.451 5056 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.16 % Allowed : 13.36 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.14 (0.14), residues: 3699 helix: 2.13 (0.20), residues: 666 sheet: 0.41 (0.16), residues: 942 loop : -0.74 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 36 HIS 0.004 0.001 HIS C 204 PHE 0.036 0.001 PHE D 29 TYR 0.016 0.001 TYR A1064 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 274 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6862 (p) REVERT: A 50 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7935 (t70) REVERT: A 87 VAL cc_start: 0.8827 (t) cc_final: 0.8548 (p) REVERT: A 197 TYR cc_start: 0.7064 (m-80) cc_final: 0.6707 (m-80) REVERT: A 336 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: A 340 ASN cc_start: 0.7546 (t0) cc_final: 0.7045 (p0) REVERT: A 354 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7861 (ttp80) REVERT: A 513 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6156 (tt0) REVERT: A 526 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7685 (mptt) REVERT: A 1014 GLU cc_start: 0.8429 (tt0) cc_final: 0.8189 (tt0) REVERT: B 26 THR cc_start: 0.6412 (OUTLIER) cc_final: 0.5960 (p) REVERT: B 27 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 81 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6610 (mp) REVERT: B 87 VAL cc_start: 0.8713 (t) cc_final: 0.8303 (p) REVERT: B 234 ARG cc_start: 0.7366 (mtt90) cc_final: 0.7148 (mtm-85) REVERT: B 295 GLU cc_start: 0.7569 (tt0) cc_final: 0.7194 (tp30) REVERT: B 302 SER cc_start: 0.9119 (t) cc_final: 0.8681 (p) REVERT: B 311 GLN cc_start: 0.7413 (tt0) cc_final: 0.6991 (tp-100) REVERT: B 336 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: B 340 ASN cc_start: 0.7436 (t0) cc_final: 0.6635 (p0) REVERT: B 354 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7835 (ttp80) REVERT: B 355 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7968 (mm) REVERT: B 475 LYS cc_start: 0.7309 (mmtt) cc_final: 0.7104 (pttt) REVERT: B 526 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7487 (mptt) REVERT: B 773 LYS cc_start: 0.8115 (tttt) cc_final: 0.7745 (tttm) REVERT: B 776 GLN cc_start: 0.7781 (tp40) cc_final: 0.7277 (tp40) REVERT: B 777 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7608 (mm-30) REVERT: B 851 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7443 (tttm) REVERT: B 897 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7977 (mtp) REVERT: B 947 ASP cc_start: 0.7504 (m-30) cc_final: 0.7179 (t0) REVERT: B 1014 GLU cc_start: 0.7977 (tt0) cc_final: 0.7608 (tt0) REVERT: B 1042 LYS cc_start: 0.8299 (mttt) cc_final: 0.7997 (mptt) REVERT: B 1111 ILE cc_start: 0.8179 (mm) cc_final: 0.7958 (tp) REVERT: B 1122 ASN cc_start: 0.8026 (p0) cc_final: 0.7790 (p0) REVERT: B 1135 TYR cc_start: 0.7482 (t80) cc_final: 0.7191 (t80) REVERT: C 26 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6664 (p) REVERT: C 81 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7061 (mp) REVERT: C 87 VAL cc_start: 0.8917 (t) cc_final: 0.8557 (p) REVERT: C 197 TYR cc_start: 0.7091 (m-80) cc_final: 0.6688 (m-10) REVERT: C 302 SER cc_start: 0.9099 (t) cc_final: 0.8809 (m) REVERT: C 311 GLN cc_start: 0.7463 (tt0) cc_final: 0.7261 (tp-100) REVERT: C 336 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: C 340 ASN cc_start: 0.7417 (t0) cc_final: 0.6818 (p0) REVERT: C 354 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7849 (ttp80) REVERT: C 526 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7680 (mptt) REVERT: C 672 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: C 1014 GLU cc_start: 0.8372 (tt0) cc_final: 0.8006 (tt0) REVERT: C 1135 TYR cc_start: 0.7710 (t80) cc_final: 0.7453 (t80) REVERT: D 23 LYS cc_start: 0.7585 (tppt) cc_final: 0.7329 (mptt) REVERT: G 35 TRP cc_start: 0.5250 (m-90) cc_final: 0.4926 (m-90) REVERT: H 64 PHE cc_start: 0.5699 (m-80) cc_final: 0.5483 (m-10) outliers start: 103 outliers final: 57 residues processed: 345 average time/residue: 1.1032 time to fit residues: 473.0866 Evaluate side-chains 329 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 258 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 932 GLN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 71 optimal weight: 0.0070 chunk 211 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 932 GLN B 516 HIS ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN C 204 HIS ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30588 Z= 0.257 Angle : 0.525 10.286 41562 Z= 0.269 Chirality : 0.045 0.198 4830 Planarity : 0.004 0.054 5295 Dihedral : 5.109 53.561 5056 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.26 % Allowed : 13.98 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.10 (0.14), residues: 3699 helix: 2.07 (0.20), residues: 666 sheet: 0.39 (0.17), residues: 927 loop : -0.75 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 36 HIS 0.004 0.001 HIS C 204 PHE 0.025 0.001 PHE C 130 TYR 0.018 0.001 TYR G 32 ARG 0.008 0.000 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 268 time to evaluate : 3.877 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 26 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6873 (p) REVERT: A 50 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7976 (t70) REVERT: A 87 VAL cc_start: 0.8839 (t) cc_final: 0.8561 (p) REVERT: A 197 TYR cc_start: 0.7104 (m-80) cc_final: 0.6684 (m-80) REVERT: A 336 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: A 340 ASN cc_start: 0.7572 (t0) cc_final: 0.7043 (p0) REVERT: A 354 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7871 (ttp80) REVERT: A 513 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6208 (tt0) REVERT: A 526 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7713 (mptt) REVERT: A 1014 GLU cc_start: 0.8444 (tt0) cc_final: 0.8206 (tt0) REVERT: B 26 THR cc_start: 0.6406 (OUTLIER) cc_final: 0.5931 (p) REVERT: B 27 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7616 (t0) REVERT: B 81 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6605 (mp) REVERT: B 87 VAL cc_start: 0.8735 (t) cc_final: 0.8312 (p) REVERT: B 234 ARG cc_start: 0.7407 (mtt90) cc_final: 0.7180 (mtm-85) REVERT: B 295 GLU cc_start: 0.7581 (tt0) cc_final: 0.7201 (tp30) REVERT: B 302 SER cc_start: 0.9133 (t) cc_final: 0.8686 (p) REVERT: B 311 GLN cc_start: 0.7402 (tt0) cc_final: 0.6995 (tp-100) REVERT: B 336 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: B 340 ASN cc_start: 0.7456 (t0) cc_final: 0.6645 (p0) REVERT: B 354 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7825 (ttp80) REVERT: B 355 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7977 (mm) REVERT: B 475 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7105 (pttt) REVERT: B 513 GLU cc_start: 0.7229 (tt0) cc_final: 0.5411 (tt0) REVERT: B 526 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7497 (mptt) REVERT: B 534 LYS cc_start: 0.7980 (mttt) cc_final: 0.7551 (mtpp) REVERT: B 773 LYS cc_start: 0.8134 (tttt) cc_final: 0.7767 (tttm) REVERT: B 776 GLN cc_start: 0.7803 (tp40) cc_final: 0.7306 (tp40) REVERT: B 777 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7618 (mm-30) REVERT: B 851 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7456 (tttm) REVERT: B 897 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7993 (mtp) REVERT: B 947 ASP cc_start: 0.7514 (m-30) cc_final: 0.7155 (t0) REVERT: B 1014 GLU cc_start: 0.8004 (tt0) cc_final: 0.7638 (tt0) REVERT: B 1042 LYS cc_start: 0.8305 (mttt) cc_final: 0.8002 (mptt) REVERT: B 1111 ILE cc_start: 0.8164 (mm) cc_final: 0.7940 (tp) REVERT: B 1122 ASN cc_start: 0.8020 (p0) cc_final: 0.7780 (p0) REVERT: B 1135 TYR cc_start: 0.7488 (t80) cc_final: 0.7197 (t80) REVERT: C 26 THR cc_start: 0.6978 (OUTLIER) cc_final: 0.6684 (p) REVERT: C 81 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7056 (mp) REVERT: C 87 VAL cc_start: 0.8921 (t) cc_final: 0.8559 (p) REVERT: C 197 TYR cc_start: 0.7143 (m-80) cc_final: 0.6701 (m-10) REVERT: C 228 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7487 (pp) REVERT: C 266 TYR cc_start: 0.8614 (m-80) cc_final: 0.8335 (m-10) REVERT: C 302 SER cc_start: 0.9108 (t) cc_final: 0.8813 (m) REVERT: C 336 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: C 340 ASN cc_start: 0.7452 (t0) cc_final: 0.6831 (p0) REVERT: C 354 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7861 (ttp80) REVERT: C 526 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7704 (mptt) REVERT: C 1014 GLU cc_start: 0.8395 (tt0) cc_final: 0.8041 (tt0) REVERT: C 1135 TYR cc_start: 0.7732 (t80) cc_final: 0.7460 (t80) REVERT: D 23 LYS cc_start: 0.7653 (tppt) cc_final: 0.7223 (mptp) REVERT: F 81 MET cc_start: 0.7768 (ttp) cc_final: 0.7398 (ttp) REVERT: G 17 ASP cc_start: 0.4008 (OUTLIER) cc_final: 0.2910 (t0) REVERT: H 64 PHE cc_start: 0.5761 (m-80) cc_final: 0.5539 (m-80) outliers start: 106 outliers final: 65 residues processed: 349 average time/residue: 1.1205 time to fit residues: 489.7639 Evaluate side-chains 339 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 259 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 302 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN B 402 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 850 GLN C 204 HIS ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN G 92 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30588 Z= 0.225 Angle : 0.512 10.605 41562 Z= 0.262 Chirality : 0.044 0.182 4830 Planarity : 0.004 0.055 5295 Dihedral : 5.039 54.495 5056 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.95 % Allowed : 14.53 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.13 (0.14), residues: 3699 helix: 2.09 (0.20), residues: 666 sheet: 0.41 (0.17), residues: 927 loop : -0.74 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 35 HIS 0.004 0.001 HIS G 55 PHE 0.023 0.001 PHE A 130 TYR 0.016 0.001 TYR A1064 ARG 0.005 0.000 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 264 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6853 (p) REVERT: A 50 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7985 (t70) REVERT: A 87 VAL cc_start: 0.8832 (t) cc_final: 0.8557 (p) REVERT: A 197 TYR cc_start: 0.7093 (m-80) cc_final: 0.6685 (m-80) REVERT: A 336 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: A 340 ASN cc_start: 0.7564 (t0) cc_final: 0.7029 (p0) REVERT: A 354 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7866 (ttp80) REVERT: A 513 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6098 (tt0) REVERT: A 526 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7703 (mptt) REVERT: A 932 GLN cc_start: 0.7549 (tt0) cc_final: 0.7258 (mt0) REVERT: A 1014 GLU cc_start: 0.8435 (tt0) cc_final: 0.8178 (tt0) REVERT: B 26 THR cc_start: 0.6379 (OUTLIER) cc_final: 0.5897 (p) REVERT: B 27 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7544 (t0) REVERT: B 81 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6601 (mp) REVERT: B 87 VAL cc_start: 0.8725 (t) cc_final: 0.8304 (p) REVERT: B 234 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7171 (mtm-85) REVERT: B 295 GLU cc_start: 0.7561 (tt0) cc_final: 0.7181 (tp30) REVERT: B 302 SER cc_start: 0.9120 (t) cc_final: 0.8692 (p) REVERT: B 311 GLN cc_start: 0.7404 (tt0) cc_final: 0.7000 (tp-100) REVERT: B 336 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: B 340 ASN cc_start: 0.7441 (t0) cc_final: 0.6622 (p0) REVERT: B 354 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7829 (ttp80) REVERT: B 355 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7971 (mm) REVERT: B 475 LYS cc_start: 0.7327 (mmtt) cc_final: 0.7105 (ptpt) REVERT: B 513 GLU cc_start: 0.7225 (tt0) cc_final: 0.5462 (tt0) REVERT: B 526 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7503 (mptt) REVERT: B 534 LYS cc_start: 0.7973 (mttt) cc_final: 0.7537 (mtpp) REVERT: B 773 LYS cc_start: 0.8126 (tttt) cc_final: 0.7754 (tttm) REVERT: B 776 GLN cc_start: 0.7806 (tp40) cc_final: 0.7299 (tp40) REVERT: B 777 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7606 (mm-30) REVERT: B 851 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7448 (tttm) REVERT: B 897 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: B 947 ASP cc_start: 0.7505 (m-30) cc_final: 0.7151 (t0) REVERT: B 1014 GLU cc_start: 0.7999 (tt0) cc_final: 0.7635 (tt0) REVERT: B 1042 LYS cc_start: 0.8287 (mttt) cc_final: 0.7984 (mptt) REVERT: B 1111 ILE cc_start: 0.8159 (mm) cc_final: 0.7937 (tp) REVERT: B 1122 ASN cc_start: 0.7978 (p0) cc_final: 0.7761 (p0) REVERT: B 1135 TYR cc_start: 0.7503 (t80) cc_final: 0.7194 (t80) REVERT: C 26 THR cc_start: 0.6955 (OUTLIER) cc_final: 0.6659 (p) REVERT: C 81 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7068 (mp) REVERT: C 87 VAL cc_start: 0.8914 (t) cc_final: 0.8548 (p) REVERT: C 197 TYR cc_start: 0.7128 (m-80) cc_final: 0.6698 (m-10) REVERT: C 228 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7485 (pp) REVERT: C 266 TYR cc_start: 0.8611 (m-80) cc_final: 0.8339 (m-10) REVERT: C 302 SER cc_start: 0.9111 (t) cc_final: 0.8823 (m) REVERT: C 336 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: C 340 ASN cc_start: 0.7451 (t0) cc_final: 0.6825 (p0) REVERT: C 354 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7832 (ttp80) REVERT: C 526 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7711 (mptt) REVERT: C 672 GLN cc_start: 0.7514 (tt0) cc_final: 0.6919 (mt0) REVERT: C 687 GLN cc_start: 0.7624 (mm-40) cc_final: 0.6968 (mm-40) REVERT: C 1014 GLU cc_start: 0.8379 (tt0) cc_final: 0.8011 (tt0) REVERT: C 1135 TYR cc_start: 0.7718 (t80) cc_final: 0.7446 (t80) REVERT: D 23 LYS cc_start: 0.7671 (tppt) cc_final: 0.7245 (mptp) REVERT: G 17 ASP cc_start: 0.4030 (OUTLIER) cc_final: 0.2931 (t0) outliers start: 96 outliers final: 63 residues processed: 337 average time/residue: 1.1360 time to fit residues: 472.3552 Evaluate side-chains 332 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 254 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 227 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 177 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 281 optimal weight: 0.4980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN C 204 HIS ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30588 Z= 0.126 Angle : 0.486 11.792 41562 Z= 0.247 Chirality : 0.043 0.195 4830 Planarity : 0.004 0.055 5295 Dihedral : 4.789 58.880 5056 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 15.85 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.30 (0.14), residues: 3699 helix: 2.33 (0.21), residues: 666 sheet: 0.48 (0.17), residues: 891 loop : -0.62 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 35 HIS 0.003 0.000 HIS C 204 PHE 0.028 0.001 PHE C 130 TYR 0.016 0.001 TYR B1064 ARG 0.003 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 272 time to evaluate : 3.840 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 26 THR cc_start: 0.6970 (OUTLIER) cc_final: 0.6739 (p) REVERT: A 87 VAL cc_start: 0.8794 (t) cc_final: 0.8503 (p) REVERT: A 340 ASN cc_start: 0.7513 (t0) cc_final: 0.6985 (p0) REVERT: A 354 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7848 (ttp80) REVERT: A 513 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6052 (tt0) REVERT: A 526 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7664 (mptt) REVERT: A 1014 GLU cc_start: 0.8371 (tt0) cc_final: 0.8116 (tt0) REVERT: B 26 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.5862 (p) REVERT: B 27 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7440 (t0) REVERT: B 81 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6618 (mp) REVERT: B 87 VAL cc_start: 0.8682 (t) cc_final: 0.8262 (p) REVERT: B 295 GLU cc_start: 0.7529 (tt0) cc_final: 0.7161 (tp30) REVERT: B 302 SER cc_start: 0.9119 (t) cc_final: 0.8703 (p) REVERT: B 311 GLN cc_start: 0.7322 (tt0) cc_final: 0.6941 (tp-100) REVERT: B 336 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7126 (p0) REVERT: B 340 ASN cc_start: 0.7381 (t0) cc_final: 0.6563 (p0) REVERT: B 354 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7806 (ttp80) REVERT: B 355 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7977 (mt) REVERT: B 475 LYS cc_start: 0.7340 (mmtt) cc_final: 0.7076 (ptmt) REVERT: B 526 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7512 (mptt) REVERT: B 653 VAL cc_start: 0.8036 (t) cc_final: 0.7802 (m) REVERT: B 718 SER cc_start: 0.8860 (m) cc_final: 0.8477 (p) REVERT: B 773 LYS cc_start: 0.8016 (tttt) cc_final: 0.7662 (tttm) REVERT: B 776 GLN cc_start: 0.7733 (tp40) cc_final: 0.7249 (tp40) REVERT: B 777 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7481 (mm-30) REVERT: B 897 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7865 (mtp) REVERT: B 947 ASP cc_start: 0.7477 (m-30) cc_final: 0.7057 (t0) REVERT: B 1014 GLU cc_start: 0.7921 (tt0) cc_final: 0.7544 (tt0) REVERT: B 1042 LYS cc_start: 0.8247 (mttt) cc_final: 0.7941 (mptt) REVERT: B 1111 ILE cc_start: 0.8168 (mm) cc_final: 0.7951 (tp) REVERT: B 1135 TYR cc_start: 0.7493 (t80) cc_final: 0.7183 (t80) REVERT: C 26 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6608 (p) REVERT: C 81 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7129 (mp) REVERT: C 87 VAL cc_start: 0.8850 (t) cc_final: 0.8491 (p) REVERT: C 197 TYR cc_start: 0.7075 (m-80) cc_final: 0.6508 (m-10) REVERT: C 228 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7457 (pp) REVERT: C 266 TYR cc_start: 0.8597 (m-80) cc_final: 0.8319 (m-10) REVERT: C 302 SER cc_start: 0.9103 (t) cc_final: 0.8835 (m) REVERT: C 336 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7483 (p0) REVERT: C 340 ASN cc_start: 0.7395 (t0) cc_final: 0.6774 (p0) REVERT: C 354 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7823 (ttp80) REVERT: C 526 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7648 (mmtt) REVERT: C 1014 GLU cc_start: 0.8315 (tt0) cc_final: 0.7960 (tt0) REVERT: C 1135 TYR cc_start: 0.7697 (t80) cc_final: 0.7401 (t80) REVERT: D 23 LYS cc_start: 0.7574 (tppt) cc_final: 0.7193 (mptp) REVERT: F 80 TYR cc_start: 0.6046 (m-10) cc_final: 0.5831 (m-10) REVERT: G 35 TRP cc_start: 0.5109 (m-90) cc_final: 0.3959 (m-90) outliers start: 66 outliers final: 40 residues processed: 316 average time/residue: 1.0942 time to fit residues: 433.0305 Evaluate side-chains 297 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 9.9990 chunk 343 optimal weight: 30.0000 chunk 313 optimal weight: 0.2980 chunk 334 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 850 GLN A 910 GLN B 351 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN C 204 HIS ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 30588 Z= 0.391 Angle : 0.593 10.279 41562 Z= 0.304 Chirality : 0.047 0.206 4830 Planarity : 0.004 0.056 5295 Dihedral : 5.427 59.580 5056 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.18 % Allowed : 15.94 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3699 helix: 1.84 (0.20), residues: 666 sheet: 0.44 (0.16), residues: 954 loop : -0.83 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 36 HIS 0.004 0.001 HIS C1061 PHE 0.035 0.002 PHE A 130 TYR 0.019 0.002 TYR A1064 ARG 0.004 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 263 time to evaluate : 4.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6838 (p) REVERT: A 87 VAL cc_start: 0.8863 (t) cc_final: 0.8594 (p) REVERT: A 197 TYR cc_start: 0.7084 (m-80) cc_final: 0.6552 (m-80) REVERT: A 239 LEU cc_start: 0.6941 (pt) cc_final: 0.6228 (tt) REVERT: A 340 ASN cc_start: 0.7606 (t0) cc_final: 0.7040 (p0) REVERT: A 354 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7891 (ttp80) REVERT: A 513 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6225 (tt0) REVERT: A 526 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7679 (mptt) REVERT: A 1014 GLU cc_start: 0.8528 (tt0) cc_final: 0.8289 (tt0) REVERT: B 26 THR cc_start: 0.6394 (OUTLIER) cc_final: 0.5931 (p) REVERT: B 27 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7605 (t0) REVERT: B 87 VAL cc_start: 0.8735 (t) cc_final: 0.8331 (p) REVERT: B 295 GLU cc_start: 0.7615 (tt0) cc_final: 0.7234 (tp30) REVERT: B 302 SER cc_start: 0.9150 (t) cc_final: 0.8697 (p) REVERT: B 311 GLN cc_start: 0.7371 (tt0) cc_final: 0.6973 (tp-100) REVERT: B 336 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: B 340 ASN cc_start: 0.7489 (t0) cc_final: 0.6645 (p0) REVERT: B 354 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7840 (ttp80) REVERT: B 475 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6988 (ptmt) REVERT: B 513 GLU cc_start: 0.7226 (tt0) cc_final: 0.5702 (tt0) REVERT: B 526 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7505 (mptt) REVERT: B 534 LYS cc_start: 0.8052 (mttt) cc_final: 0.7643 (mtpp) REVERT: B 773 LYS cc_start: 0.8129 (tttt) cc_final: 0.7737 (tttm) REVERT: B 777 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7667 (mm-30) REVERT: B 851 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7424 (tttm) REVERT: B 947 ASP cc_start: 0.7578 (m-30) cc_final: 0.7252 (t0) REVERT: B 1014 GLU cc_start: 0.8092 (tt0) cc_final: 0.7735 (tt0) REVERT: B 1042 LYS cc_start: 0.8338 (mttt) cc_final: 0.8002 (mptt) REVERT: B 1111 ILE cc_start: 0.8142 (mm) cc_final: 0.7914 (tp) REVERT: B 1135 TYR cc_start: 0.7495 (t80) cc_final: 0.7206 (t80) REVERT: C 26 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6675 (p) REVERT: C 87 VAL cc_start: 0.8933 (t) cc_final: 0.8577 (p) REVERT: C 197 TYR cc_start: 0.7100 (m-80) cc_final: 0.6660 (m-10) REVERT: C 228 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 295 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7713 (tp30) REVERT: C 302 SER cc_start: 0.9114 (t) cc_final: 0.8822 (m) REVERT: C 336 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: C 340 ASN cc_start: 0.7510 (t0) cc_final: 0.6863 (p0) REVERT: C 354 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7853 (ttp80) REVERT: C 526 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7681 (mmtt) REVERT: C 534 LYS cc_start: 0.8248 (mttt) cc_final: 0.8045 (mtpp) REVERT: C 1014 GLU cc_start: 0.8452 (tt0) cc_final: 0.8066 (tt0) REVERT: D 23 LYS cc_start: 0.7671 (tppt) cc_final: 0.7342 (mptt) outliers start: 71 outliers final: 43 residues processed: 320 average time/residue: 1.0823 time to fit residues: 429.6952 Evaluate side-chains 304 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.0370 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 0.0970 chunk 370 optimal weight: 6.9990 chunk 341 optimal weight: 0.9980 chunk 295 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 227 optimal weight: 0.3980 chunk 180 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 850 GLN B 911 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 910 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 30588 Z= 0.145 Angle : 0.507 10.188 41562 Z= 0.257 Chirality : 0.043 0.167 4830 Planarity : 0.004 0.064 5295 Dihedral : 4.908 56.238 5056 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.44 % Allowed : 16.93 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.22 (0.14), residues: 3699 helix: 2.21 (0.21), residues: 666 sheet: 0.50 (0.17), residues: 945 loop : -0.71 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 36 HIS 0.004 0.001 HIS L 92 PHE 0.029 0.001 PHE C 130 TYR 0.020 0.001 TYR D 80 ARG 0.005 0.000 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6771 (p) REVERT: A 87 VAL cc_start: 0.8822 (t) cc_final: 0.8531 (p) REVERT: A 340 ASN cc_start: 0.7480 (t0) cc_final: 0.6953 (p0) REVERT: A 354 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7867 (ttp80) REVERT: A 513 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6097 (tt0) REVERT: A 526 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7672 (mptt) REVERT: A 1014 GLU cc_start: 0.8410 (tt0) cc_final: 0.8171 (tt0) REVERT: B 26 THR cc_start: 0.6338 (OUTLIER) cc_final: 0.5861 (p) REVERT: B 27 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7485 (t0) REVERT: B 81 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6691 (mp) REVERT: B 87 VAL cc_start: 0.8701 (t) cc_final: 0.8284 (p) REVERT: B 302 SER cc_start: 0.9148 (t) cc_final: 0.8710 (m) REVERT: B 311 GLN cc_start: 0.7289 (tt0) cc_final: 0.6906 (tp-100) REVERT: B 336 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7193 (p0) REVERT: B 340 ASN cc_start: 0.7386 (t0) cc_final: 0.6563 (p0) REVERT: B 354 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7808 (ttp80) REVERT: B 513 GLU cc_start: 0.7106 (tt0) cc_final: 0.6695 (tt0) REVERT: B 526 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7494 (mptt) REVERT: B 653 VAL cc_start: 0.8046 (t) cc_final: 0.7791 (m) REVERT: B 773 LYS cc_start: 0.8091 (tttt) cc_final: 0.7705 (tttm) REVERT: B 776 GLN cc_start: 0.7746 (tp40) cc_final: 0.7272 (tp40) REVERT: B 777 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7550 (mm-30) REVERT: B 947 ASP cc_start: 0.7496 (m-30) cc_final: 0.7119 (t0) REVERT: B 1014 GLU cc_start: 0.8027 (tt0) cc_final: 0.7662 (tt0) REVERT: B 1042 LYS cc_start: 0.8249 (mttt) cc_final: 0.7957 (mptt) REVERT: B 1111 ILE cc_start: 0.8146 (mm) cc_final: 0.7933 (tp) REVERT: B 1135 TYR cc_start: 0.7495 (t80) cc_final: 0.7198 (t80) REVERT: C 26 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6575 (p) REVERT: C 81 LEU cc_start: 0.7479 (mm) cc_final: 0.7155 (mp) REVERT: C 87 VAL cc_start: 0.8873 (t) cc_final: 0.8516 (p) REVERT: C 197 TYR cc_start: 0.7098 (m-80) cc_final: 0.6677 (m-10) REVERT: C 228 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7458 (pp) REVERT: C 266 TYR cc_start: 0.8614 (m-80) cc_final: 0.8350 (m-10) REVERT: C 302 SER cc_start: 0.9120 (t) cc_final: 0.8842 (m) REVERT: C 336 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: C 340 ASN cc_start: 0.7407 (t0) cc_final: 0.6736 (p0) REVERT: C 354 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7826 (ttp80) REVERT: C 526 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7740 (mptt) REVERT: C 1014 GLU cc_start: 0.8338 (tt0) cc_final: 0.7991 (tt0) REVERT: H 48 MET cc_start: 0.6517 (mpp) cc_final: 0.6136 (mpp) outliers start: 47 outliers final: 36 residues processed: 289 average time/residue: 1.1569 time to fit residues: 415.6825 Evaluate side-chains 294 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 250 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125216 restraints weight = 38517.566| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.43 r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30588 Z= 0.184 Angle : 0.510 10.629 41562 Z= 0.259 Chirality : 0.044 0.178 4830 Planarity : 0.004 0.059 5295 Dihedral : 4.775 55.785 5056 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.63 % Allowed : 16.80 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3699 helix: 2.24 (0.21), residues: 666 sheet: 0.34 (0.17), residues: 963 loop : -0.67 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP H 36 HIS 0.004 0.001 HIS L 92 PHE 0.037 0.001 PHE B 130 TYR 0.024 0.001 TYR E 32 ARG 0.005 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10132.09 seconds wall clock time: 183 minutes 38.76 seconds (11018.76 seconds total)