Starting phenix.real_space_refine on Thu Mar 21 19:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9i_13870/03_2024/7q9i_13870.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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 138 5.16 5 C 19693 2.51 5 N 5098 2.21 5 O 6037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30966 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8290 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 6 Chain: "B" Number of atoms: 8267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8267 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.21, per 1000 atoms: 0.49 Number of scatterers: 30966 At special positions: 0 Unit cell: (205.84, 192.56, 190.9, 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 138 16.00 O 6037 8.00 N 5098 7.00 C 19693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 106 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 106 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 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 340 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " 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 C1309 " - " ASN C 340 " " NAG D 1 " - " ASN A 714 " " NAG G 1 " - " ASN A 798 " " NAG I 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: 11.50 Conformation dependent library (CDL) restraints added in 5.3 seconds 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 72 sheets defined 22.2% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.290A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.592A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.301A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.521A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 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 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.043A 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 1031 removed outlier: 4.331A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.235A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.692A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.199A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 741 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 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.833A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.002A 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 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.594A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.061A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.948A 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 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.555A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.485A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 741 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: 3.896A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.835A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.908A 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 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.801A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.524A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1031 removed outlier: 3.945A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.852A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.421A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.816A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.917A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.917A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.889A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.416A 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=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 3.913A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.533A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.146A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.024A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.801A 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: 4.382A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.507A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.586A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 260 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.786A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.896A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.896A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.368A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.793A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.793A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AD1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.730A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.659A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.994A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD6, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD7, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.083A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.434A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.517A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.735A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.857A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.902A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.902A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.288A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 325 removed outlier: 3.864A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.743A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.731A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.385A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.978A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.397A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.527A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.776A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.204A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.709A pdb=" N VAL L 70 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.519A pdb=" N ILE L 47 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AG7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.775A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.203A pdb=" N VAL E 115 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.709A pdb=" N VAL F 70 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.519A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AH4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.776A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.203A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 4 through 5 removed outlier: 4.710A pdb=" N VAL K 70 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.518A pdb=" N ILE K 47 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN K 36 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU K 45 " --> pdb=" O GLN K 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 9 through 12 1379 hydrogen bonds defined for protein. 3654 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: 15.09 Time building geometry restraints manager: 12.55 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: 9846 1.34 - 1.46: 7862 1.46 - 1.58: 13807 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 31689 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C ILE B 802 " pdb=" N LEU B 803 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.83e-02 1.25e+03 4.10e+00 bond pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " ideal model delta sigma weight residual 1.530 1.561 -0.032 1.58e-02 4.01e+03 3.98e+00 ... (remaining 31684 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 871 106.42 - 113.35: 17390 113.35 - 120.27: 10898 120.27 - 127.20: 13657 127.20 - 134.12: 308 Bond angle restraints: 43124 Sorted by residual: angle pdb=" C VAL B 317 " pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta sigma weight residual 121.80 131.15 -9.35 2.44e+00 1.68e-01 1.47e+01 angle pdb=" N GLN B 318 " pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " ideal model delta sigma weight residual 110.37 116.19 -5.82 1.78e+00 3.16e-01 1.07e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.62 110.93 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" C CYS F 22 " pdb=" N GLY F 23 " pdb=" CA GLY F 23 " ideal model delta sigma weight residual 122.29 119.46 2.83 8.90e-01 1.26e+00 1.01e+01 angle pdb=" C CYS L 22 " pdb=" N GLY L 23 " pdb=" CA GLY L 23 " ideal model delta sigma weight residual 122.29 119.47 2.82 8.90e-01 1.26e+00 1.01e+01 ... (remaining 43119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18311 17.73 - 35.47: 840 35.47 - 53.20: 202 53.20 - 70.93: 43 70.93 - 88.66: 13 Dihedral angle restraints: 19409 sinusoidal: 8182 harmonic: 11227 Sorted by residual: dihedral pdb=" CA LYS B 525 " pdb=" C LYS B 525 " pdb=" N LYS B 526 " pdb=" CA LYS B 526 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ILE B 329 " pdb=" C ILE B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -125.70 39.70 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 19406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4080 0.051 - 0.102: 685 0.102 - 0.154: 209 0.154 - 0.205: 7 0.205 - 0.256: 2 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.43e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.48e+00 ... (remaining 4980 not shown) Planarity restraints: 5550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.39e+00 pdb=" CG ASN A 328 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 585 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 586 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1049 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1050 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " -0.024 5.00e-02 4.00e+02 ... (remaining 5547 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3552 2.75 - 3.29: 30318 3.29 - 3.83: 51650 3.83 - 4.36: 64357 4.36 - 4.90: 107875 Nonbonded interactions: 257752 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb=" OD1 ASP B 53 " model vdw 2.216 3.040 nonbonded pdb=" O LYS C 961 " pdb=" OG SER C 964 " model vdw 2.220 2.440 nonbonded pdb=" O PRO A 57 " pdb=" OG SER A 60 " model vdw 2.225 2.440 nonbonded pdb=" O ALA A 876 " pdb=" OG1 THR A 880 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.241 2.440 ... (remaining 257747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 617 or resid 638 through 1144 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 13 through 1144 or resid 1301 through 1309)) selection = (chain 'C' and (resid 13 through 617 or resid 638 through 1144 or resid 1301 thr \ ough 1309)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' 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' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.030 Extract box with map and model: 5.810 Check model and map are aligned: 0.380 Set scattering table: 0.280 Process input model: 80.280 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 0.057 31689 Z= 0.242 Angle : 0.574 9.346 43124 Z= 0.313 Chirality : 0.044 0.256 4983 Planarity : 0.004 0.043 5509 Dihedral : 11.095 88.664 12078 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.80 % Allowed : 4.08 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 3827 helix: 1.38 (0.21), residues: 665 sheet: -0.28 (0.15), residues: 1045 loop : -0.68 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.004 0.001 HIS A 652 PHE 0.016 0.001 PHE C 303 TYR 0.013 0.001 TYR A 366 ARG 0.003 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 764 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8535 (p) cc_final: 0.7767 (m) REVERT: A 52 GLN cc_start: 0.8906 (tt0) cc_final: 0.8641 (tp-100) REVERT: A 117 LEU cc_start: 0.9519 (tp) cc_final: 0.9254 (tp) REVERT: A 225 PRO cc_start: 0.7868 (Cg_exo) cc_final: 0.7535 (Cg_endo) REVERT: A 325 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.6713 (tpp80) REVERT: A 409 PRO cc_start: 0.8920 (Cg_endo) cc_final: 0.8310 (Cg_exo) REVERT: A 420 TYR cc_start: 0.8317 (t80) cc_final: 0.7550 (t80) REVERT: A 453 PHE cc_start: 0.9268 (m-80) cc_final: 0.8912 (m-80) REVERT: A 457 ASN cc_start: 0.9590 (m-40) cc_final: 0.9213 (t0) REVERT: A 529 ASN cc_start: 0.9611 (m-40) cc_final: 0.9282 (p0) REVERT: A 568 ASP cc_start: 0.9469 (m-30) cc_final: 0.8392 (t0) REVERT: A 715 PHE cc_start: 0.8027 (p90) cc_final: 0.7573 (p90) REVERT: A 727 SER cc_start: 0.9209 (p) cc_final: 0.8830 (t) REVERT: A 729 THR cc_start: 0.9126 (m) cc_final: 0.8882 (t) REVERT: A 737 MET cc_start: 0.9023 (tpt) cc_final: 0.8655 (tpp) REVERT: A 745 GLU cc_start: 0.8846 (mp0) cc_final: 0.7998 (tt0) REVERT: A 756 PHE cc_start: 0.8706 (m-10) cc_final: 0.8470 (m-10) REVERT: A 771 GLN cc_start: 0.9235 (mm-40) cc_final: 0.9029 (mm-40) REVERT: A 774 ASN cc_start: 0.9333 (m-40) cc_final: 0.9114 (m-40) REVERT: A 779 PHE cc_start: 0.8912 (m-80) cc_final: 0.8553 (m-80) REVERT: A 816 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9104 (mt-10) REVERT: A 823 VAL cc_start: 0.8696 (t) cc_final: 0.7634 (t) REVERT: A 903 PHE cc_start: 0.9069 (m-80) cc_final: 0.8481 (m-10) REVERT: A 908 VAL cc_start: 0.8460 (t) cc_final: 0.8076 (t) REVERT: A 910 GLN cc_start: 0.8295 (pt0) cc_final: 0.8049 (pp30) REVERT: A 918 LYS cc_start: 0.9715 (mttt) cc_final: 0.9499 (tptp) REVERT: A 932 GLN cc_start: 0.9189 (mt0) cc_final: 0.8811 (tm-30) REVERT: A 944 LYS cc_start: 0.9523 (mttt) cc_final: 0.9320 (mmmm) REVERT: A 998 LEU cc_start: 0.9530 (tp) cc_final: 0.9245 (pp) REVERT: A 1007 GLN cc_start: 0.9487 (mm-40) cc_final: 0.8910 (tp40) REVERT: A 1085 HIS cc_start: 0.9135 (m-70) cc_final: 0.8852 (m90) REVERT: A 1116 ASN cc_start: 0.9302 (m-40) cc_final: 0.8970 (m110) REVERT: B 128 ILE cc_start: 0.9548 (mt) cc_final: 0.9333 (mp) REVERT: B 177 MET cc_start: -0.1519 (ttm) cc_final: -0.5037 (mmt) REVERT: B 223 LEU cc_start: 0.9032 (mp) cc_final: 0.8673 (mm) REVERT: B 272 PHE cc_start: 0.7942 (m-80) cc_final: 0.7380 (m-80) REVERT: B 297 LYS cc_start: 0.9482 (mttt) cc_final: 0.9198 (mtpp) REVERT: B 340 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8771 (m-40) REVERT: B 384 LEU cc_start: 0.9620 (mt) cc_final: 0.9374 (mm) REVERT: B 565 ASP cc_start: 0.9027 (t0) cc_final: 0.8228 (p0) REVERT: B 609 TYR cc_start: 0.9030 (m-80) cc_final: 0.8659 (m-80) REVERT: B 655 ASN cc_start: 0.8385 (m-40) cc_final: 0.7831 (t0) REVERT: B 717 ILE cc_start: 0.8235 (mm) cc_final: 0.7252 (mm) REVERT: B 738 TYR cc_start: 0.8674 (t80) cc_final: 0.8451 (t80) REVERT: B 762 ARG cc_start: 0.9350 (ttm110) cc_final: 0.8670 (mtm-85) REVERT: B 774 ASN cc_start: 0.9285 (m-40) cc_final: 0.8787 (m-40) REVERT: B 865 GLU cc_start: 0.9256 (tt0) cc_final: 0.8952 (pm20) REVERT: B 928 ILE cc_start: 0.9003 (mm) cc_final: 0.8565 (pt) REVERT: B 932 GLN cc_start: 0.8915 (mt0) cc_final: 0.8426 (tm-30) REVERT: B 944 LYS cc_start: 0.9489 (mttt) cc_final: 0.9262 (mtmt) REVERT: B 961 LYS cc_start: 0.9699 (mttt) cc_final: 0.9438 (mmtm) REVERT: B 963 LEU cc_start: 0.8472 (mt) cc_final: 0.7998 (mt) REVERT: B 989 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8598 (mm110) REVERT: B 1028 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 1051 GLN cc_start: 0.8601 (mm-40) cc_final: 0.7630 (mm-40) REVERT: B 1069 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 1085 HIS cc_start: 0.7776 (m-70) cc_final: 0.7522 (m90) REVERT: B 1106 PHE cc_start: 0.8762 (t80) cc_final: 0.7644 (t80) REVERT: C 44 ARG cc_start: 0.4263 (OUTLIER) cc_final: 0.4061 (mpt-90) REVERT: C 55 PHE cc_start: 0.8084 (m-80) cc_final: 0.6846 (m-80) REVERT: C 56 LEU cc_start: 0.9213 (tp) cc_final: 0.9002 (tp) REVERT: C 58 PHE cc_start: 0.9071 (m-10) cc_final: 0.8760 (m-80) REVERT: C 128 ILE cc_start: 0.9549 (mt) cc_final: 0.9247 (mt) REVERT: C 177 MET cc_start: -0.0392 (ttm) cc_final: -0.1292 (ttt) REVERT: C 223 LEU cc_start: 0.9351 (mp) cc_final: 0.8985 (mp) REVERT: C 348 TYR cc_start: 0.9122 (p90) cc_final: 0.8820 (p90) REVERT: C 362 TYR cc_start: 0.9287 (m-80) cc_final: 0.8399 (m-10) REVERT: C 707 ASN cc_start: 0.9029 (p0) cc_final: 0.8320 (t0) REVERT: C 744 THR cc_start: 0.9566 (m) cc_final: 0.9301 (p) REVERT: C 748 ASN cc_start: 0.9286 (m-40) cc_final: 0.9055 (m110) REVERT: C 761 ASN cc_start: 0.9120 (m110) cc_final: 0.8652 (m110) REVERT: C 799 PHE cc_start: 0.8586 (m-80) cc_final: 0.8386 (m-80) REVERT: C 819 LEU cc_start: 0.9623 (mt) cc_final: 0.9344 (mt) REVERT: C 858 LEU cc_start: 0.8935 (mt) cc_final: 0.8514 (tt) REVERT: C 918 LYS cc_start: 0.9566 (mttt) cc_final: 0.9201 (mptt) REVERT: C 961 LYS cc_start: 0.9365 (mttt) cc_final: 0.9037 (mmtt) REVERT: C 983 PRO cc_start: 0.8241 (Cg_exo) cc_final: 0.7851 (Cg_endo) REVERT: C 1015 ILE cc_start: 0.9632 (mm) cc_final: 0.9251 (tp) REVERT: C 1073 THR cc_start: 0.9053 (m) cc_final: 0.8439 (p) REVERT: C 1106 PHE cc_start: 0.8762 (t80) cc_final: 0.8178 (t80) REVERT: C 1108 GLU cc_start: 0.9106 (tt0) cc_final: 0.8679 (pp20) REVERT: C 1110 GLN cc_start: 0.9614 (mt0) cc_final: 0.9201 (mm110) REVERT: E 34 MET cc_start: -0.4603 (mmm) cc_final: -0.4896 (mmt) outliers start: 27 outliers final: 8 residues processed: 787 average time/residue: 0.4389 time to fit residues: 538.6158 Evaluate side-chains 500 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 489 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 50.0000 chunk 289 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 299 optimal weight: 0.0870 chunk 115 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 484 ASN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1008 GLN A1051 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 268 GLN B 447 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B 952 ASN B1085 HIS ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 604 GLN C 652 HIS ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 904 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1055 HIS ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN F 96 HIS K 26 ASN ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31689 Z= 0.327 Angle : 0.712 10.164 43124 Z= 0.384 Chirality : 0.047 0.314 4983 Planarity : 0.005 0.043 5509 Dihedral : 6.642 52.666 5297 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.30 % Allowed : 2.47 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3827 helix: 0.30 (0.18), residues: 688 sheet: -0.14 (0.15), residues: 1096 loop : -0.67 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 52 HIS 0.010 0.001 HIS B 652 PHE 0.042 0.003 PHE A 562 TYR 0.027 0.002 TYR B 738 ARG 0.013 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 558 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8566 (p) cc_final: 0.7834 (m) REVERT: A 409 PRO cc_start: 0.8978 (Cg_endo) cc_final: 0.8676 (Cg_exo) REVERT: A 420 TYR cc_start: 0.8076 (t80) cc_final: 0.7085 (t80) REVERT: A 453 PHE cc_start: 0.9329 (m-80) cc_final: 0.8948 (m-80) REVERT: A 529 ASN cc_start: 0.9638 (m-40) cc_final: 0.9344 (p0) REVERT: A 532 LYS cc_start: 0.9211 (mttt) cc_final: 0.8969 (ptmt) REVERT: A 568 ASP cc_start: 0.9540 (m-30) cc_final: 0.8559 (t0) REVERT: A 609 TYR cc_start: 0.8477 (m-80) cc_final: 0.8211 (m-80) REVERT: A 728 MET cc_start: 0.9257 (ptt) cc_final: 0.9046 (ptt) REVERT: A 737 MET cc_start: 0.9010 (tpt) cc_final: 0.8705 (tpp) REVERT: A 745 GLU cc_start: 0.9080 (mp0) cc_final: 0.8318 (tt0) REVERT: A 753 TYR cc_start: 0.8927 (m-10) cc_final: 0.8659 (m-10) REVERT: A 759 GLN cc_start: 0.9657 (pt0) cc_final: 0.9390 (pp30) REVERT: A 760 LEU cc_start: 0.9462 (mt) cc_final: 0.8820 (mt) REVERT: A 773 LYS cc_start: 0.9522 (mttm) cc_final: 0.9218 (mtpp) REVERT: A 823 VAL cc_start: 0.8254 (t) cc_final: 0.7905 (t) REVERT: A 908 VAL cc_start: 0.8020 (t) cc_final: 0.7730 (t) REVERT: A 916 ASN cc_start: 0.9180 (m-40) cc_final: 0.8965 (m110) REVERT: A 918 LYS cc_start: 0.9747 (mttt) cc_final: 0.9376 (tppt) REVERT: A 944 LYS cc_start: 0.9519 (mttt) cc_final: 0.9317 (mmmm) REVERT: A 954 GLN cc_start: 0.9532 (mt0) cc_final: 0.9290 (mt0) REVERT: A 957 ASN cc_start: 0.9511 (m110) cc_final: 0.9310 (m110) REVERT: A 963 LEU cc_start: 0.9493 (mt) cc_final: 0.9276 (tt) REVERT: A 966 ASN cc_start: 0.9407 (p0) cc_final: 0.9146 (p0) REVERT: A 971 SER cc_start: 0.7246 (t) cc_final: 0.6652 (p) REVERT: A 994 ILE cc_start: 0.8800 (mt) cc_final: 0.8552 (mt) REVERT: A 999 GLN cc_start: 0.9372 (tp-100) cc_final: 0.8885 (tp-100) REVERT: A 1002 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9174 (tp-100) REVERT: A 1007 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8932 (tm-30) REVERT: A 1047 MET cc_start: 0.7667 (ttm) cc_final: 0.6485 (mtt) REVERT: A 1085 HIS cc_start: 0.9162 (m-70) cc_final: 0.8938 (m-70) REVERT: A 1116 ASN cc_start: 0.9185 (m-40) cc_final: 0.8976 (m110) REVERT: A 1124 ASP cc_start: 0.8386 (p0) cc_final: 0.8149 (p0) REVERT: B 106 PHE cc_start: 0.8613 (m-80) cc_final: 0.8133 (m-80) REVERT: B 117 LEU cc_start: 0.9832 (tp) cc_final: 0.9523 (tp) REVERT: B 118 LEU cc_start: 0.9609 (tp) cc_final: 0.9361 (tp) REVERT: B 153 MET cc_start: 0.8216 (tmm) cc_final: 0.8004 (mtt) REVERT: B 177 MET cc_start: -0.1493 (ttm) cc_final: -0.4450 (mmt) REVERT: B 272 PHE cc_start: 0.8413 (m-80) cc_final: 0.7586 (m-80) REVERT: B 297 LYS cc_start: 0.9584 (mttt) cc_final: 0.9260 (mtpp) REVERT: B 362 TYR cc_start: 0.9564 (m-80) cc_final: 0.9199 (m-80) REVERT: B 384 LEU cc_start: 0.9701 (mt) cc_final: 0.9390 (mm) REVERT: B 529 ASN cc_start: 0.9509 (p0) cc_final: 0.9303 (p0) REVERT: B 555 LYS cc_start: 0.8595 (tptt) cc_final: 0.8101 (ttpt) REVERT: B 565 ASP cc_start: 0.9212 (t0) cc_final: 0.8211 (p0) REVERT: B 609 TYR cc_start: 0.9267 (m-80) cc_final: 0.8720 (m-80) REVERT: B 655 ASN cc_start: 0.8430 (m-40) cc_final: 0.7773 (t0) REVERT: B 717 ILE cc_start: 0.8414 (mm) cc_final: 0.7514 (mm) REVERT: B 770 GLU cc_start: 0.8932 (tp30) cc_final: 0.8489 (tp30) REVERT: B 774 ASN cc_start: 0.9254 (m-40) cc_final: 0.8839 (m-40) REVERT: B 802 ILE cc_start: 0.8685 (pt) cc_final: 0.8447 (pt) REVERT: B 865 GLU cc_start: 0.9328 (tt0) cc_final: 0.8913 (mp0) REVERT: B 930 LYS cc_start: 0.9628 (mmtt) cc_final: 0.9317 (mmmm) REVERT: B 989 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8035 (mm-40) REVERT: B 1001 LEU cc_start: 0.9123 (mt) cc_final: 0.8710 (mt) REVERT: B 1009 LEU cc_start: 0.9522 (mt) cc_final: 0.9180 (mt) REVERT: B 1051 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8604 (mm-40) REVERT: B 1106 PHE cc_start: 0.8748 (t80) cc_final: 0.8168 (t80) REVERT: C 53 ASP cc_start: 0.8914 (m-30) cc_final: 0.8695 (m-30) REVERT: C 55 PHE cc_start: 0.7945 (m-80) cc_final: 0.6672 (m-10) REVERT: C 177 MET cc_start: 0.0963 (ttm) cc_final: 0.0408 (ttt) REVERT: C 348 TYR cc_start: 0.9220 (p90) cc_final: 0.8918 (p90) REVERT: C 377 TYR cc_start: 0.7861 (m-80) cc_final: 0.7258 (m-80) REVERT: C 707 ASN cc_start: 0.9218 (p0) cc_final: 0.8463 (t0) REVERT: C 761 ASN cc_start: 0.9404 (m110) cc_final: 0.9160 (p0) REVERT: C 774 ASN cc_start: 0.9465 (m-40) cc_final: 0.9245 (m-40) REVERT: C 779 PHE cc_start: 0.9222 (m-80) cc_final: 0.8638 (m-80) REVERT: C 803 LEU cc_start: 0.9683 (mt) cc_final: 0.9289 (pp) REVERT: C 816 GLU cc_start: 0.9034 (mt-10) cc_final: 0.7012 (mt-10) REVERT: C 819 LEU cc_start: 0.9589 (mt) cc_final: 0.9296 (mt) REVERT: C 820 PHE cc_start: 0.8094 (m-80) cc_final: 0.7694 (m-80) REVERT: C 853 ASN cc_start: 0.8843 (m-40) cc_final: 0.8614 (m110) REVERT: C 918 LYS cc_start: 0.9622 (mttt) cc_final: 0.9298 (mptt) REVERT: C 923 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: C 961 LYS cc_start: 0.9468 (mttt) cc_final: 0.9068 (mmtt) REVERT: C 1009 LEU cc_start: 0.9590 (mt) cc_final: 0.9359 (mm) REVERT: C 1014 GLU cc_start: 0.9045 (pt0) cc_final: 0.8590 (pp20) REVERT: C 1028 GLU cc_start: 0.8804 (tp30) cc_final: 0.8536 (tp30) REVERT: C 1051 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8053 (tp-100) REVERT: C 1085 HIS cc_start: 0.8956 (m-70) cc_final: 0.8441 (m-70) REVERT: H 32 TYR cc_start: 0.9079 (m-80) cc_final: 0.8735 (m-80) REVERT: H 34 MET cc_start: 0.3266 (mpp) cc_final: 0.2905 (mpp) REVERT: H 83 MET cc_start: -0.7001 (ptt) cc_final: -0.7322 (ptt) outliers start: 10 outliers final: 1 residues processed: 563 average time/residue: 0.4407 time to fit residues: 404.7414 Evaluate side-chains 434 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 432 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 347 optimal weight: 30.0000 chunk 375 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 344 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1002 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 821 ASN B 904 ASN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN C 164 ASN C 687 GLN ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 GLN ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31689 Z= 0.284 Angle : 0.628 12.099 43124 Z= 0.340 Chirality : 0.044 0.350 4983 Planarity : 0.004 0.042 5509 Dihedral : 5.994 53.867 5297 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3827 helix: 0.28 (0.19), residues: 685 sheet: -0.06 (0.15), residues: 1056 loop : -0.70 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 34 HIS 0.009 0.002 HIS L 96 PHE 0.030 0.002 PHE B 58 TYR 0.027 0.002 TYR C 310 ARG 0.014 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8619 (p) cc_final: 0.7492 (m) REVERT: A 420 TYR cc_start: 0.8493 (t80) cc_final: 0.7711 (t80) REVERT: A 453 PHE cc_start: 0.9252 (m-80) cc_final: 0.8968 (m-10) REVERT: A 529 ASN cc_start: 0.9626 (m-40) cc_final: 0.9340 (p0) REVERT: A 568 ASP cc_start: 0.9629 (m-30) cc_final: 0.8651 (t0) REVERT: A 738 TYR cc_start: 0.8964 (t80) cc_final: 0.8721 (t80) REVERT: A 745 GLU cc_start: 0.9152 (mp0) cc_final: 0.8422 (tt0) REVERT: A 753 TYR cc_start: 0.9177 (m-10) cc_final: 0.8614 (m-10) REVERT: A 756 PHE cc_start: 0.8835 (m-10) cc_final: 0.8344 (m-10) REVERT: A 759 GLN cc_start: 0.9735 (pt0) cc_final: 0.9498 (pp30) REVERT: A 760 LEU cc_start: 0.9603 (mt) cc_final: 0.8841 (mt) REVERT: A 769 VAL cc_start: 0.9557 (t) cc_final: 0.9261 (p) REVERT: A 773 LYS cc_start: 0.9487 (mttm) cc_final: 0.9046 (mtmm) REVERT: A 823 VAL cc_start: 0.8649 (t) cc_final: 0.8440 (t) REVERT: A 916 ASN cc_start: 0.9124 (m-40) cc_final: 0.8918 (m110) REVERT: A 918 LYS cc_start: 0.9720 (mttt) cc_final: 0.9280 (tppt) REVERT: A 944 LYS cc_start: 0.9476 (mttt) cc_final: 0.9203 (mmmm) REVERT: A 954 GLN cc_start: 0.9484 (mt0) cc_final: 0.9190 (pt0) REVERT: A 957 ASN cc_start: 0.9475 (m110) cc_final: 0.9217 (m110) REVERT: A 962 GLN cc_start: 0.9148 (mm110) cc_final: 0.8735 (mm110) REVERT: A 963 LEU cc_start: 0.9558 (mt) cc_final: 0.9199 (tt) REVERT: A 966 ASN cc_start: 0.9541 (p0) cc_final: 0.8869 (m-40) REVERT: A 989 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8387 (mm-40) REVERT: A 999 GLN cc_start: 0.9324 (tp-100) cc_final: 0.8766 (tp-100) REVERT: A 1002 GLN cc_start: 0.9568 (tp40) cc_final: 0.9172 (tp-100) REVERT: A 1007 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8825 (tm-30) REVERT: A 1047 MET cc_start: 0.7991 (ttm) cc_final: 0.6892 (mtt) REVERT: A 1085 HIS cc_start: 0.9224 (m-70) cc_final: 0.8794 (m90) REVERT: B 153 MET cc_start: 0.8384 (tmm) cc_final: 0.8037 (mtt) REVERT: B 177 MET cc_start: -0.0120 (ttm) cc_final: -0.3941 (mmt) REVERT: B 297 LYS cc_start: 0.9630 (mttt) cc_final: 0.9418 (mtpp) REVERT: B 315 PHE cc_start: 0.8819 (t80) cc_final: 0.8479 (t80) REVERT: B 362 TYR cc_start: 0.9505 (m-80) cc_final: 0.9170 (m-80) REVERT: B 529 ASN cc_start: 0.9456 (p0) cc_final: 0.9240 (p0) REVERT: B 551 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9059 (mm-30) REVERT: B 555 LYS cc_start: 0.8276 (tptt) cc_final: 0.7867 (ttpt) REVERT: B 565 ASP cc_start: 0.9226 (t0) cc_final: 0.8087 (p0) REVERT: B 609 TYR cc_start: 0.9231 (m-80) cc_final: 0.8896 (m-80) REVERT: B 610 GLN cc_start: 0.8143 (tp40) cc_final: 0.7507 (tp40) REVERT: B 655 ASN cc_start: 0.8469 (m-40) cc_final: 0.7805 (t0) REVERT: B 717 ILE cc_start: 0.8394 (mm) cc_final: 0.7729 (mm) REVERT: B 781 GLN cc_start: 0.8918 (mm110) cc_final: 0.8452 (mm110) REVERT: B 865 GLU cc_start: 0.9370 (tt0) cc_final: 0.8954 (mp0) REVERT: B 930 LYS cc_start: 0.9663 (mmtt) cc_final: 0.9289 (mmmm) REVERT: B 957 ASN cc_start: 0.9395 (m110) cc_final: 0.9139 (m110) REVERT: B 999 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8849 (tm-30) REVERT: B 1001 LEU cc_start: 0.9189 (mt) cc_final: 0.8981 (mt) REVERT: B 1009 LEU cc_start: 0.9534 (mt) cc_final: 0.9160 (mt) REVERT: B 1051 GLN cc_start: 0.8711 (mm-40) cc_final: 0.7687 (mm-40) REVERT: B 1064 TYR cc_start: 0.8981 (t80) cc_final: 0.8636 (t80) REVERT: B 1106 PHE cc_start: 0.8794 (t80) cc_final: 0.8292 (t80) REVERT: C 58 PHE cc_start: 0.9295 (m-10) cc_final: 0.8959 (m-80) REVERT: C 177 MET cc_start: 0.2040 (ttm) cc_final: 0.1438 (ttt) REVERT: C 189 LEU cc_start: 0.9588 (tp) cc_final: 0.8770 (tp) REVERT: C 191 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8155 (mp0) REVERT: C 223 LEU cc_start: 0.9327 (mp) cc_final: 0.9070 (mp) REVERT: C 272 PHE cc_start: 0.7748 (m-10) cc_final: 0.7547 (m-10) REVERT: C 321 GLU cc_start: 0.9239 (tp30) cc_final: 0.8589 (tp30) REVERT: C 348 TYR cc_start: 0.9258 (p90) cc_final: 0.8955 (p90) REVERT: C 612 VAL cc_start: 0.8866 (t) cc_final: 0.8664 (m) REVERT: C 707 ASN cc_start: 0.9251 (p0) cc_final: 0.8649 (t0) REVERT: C 733 VAL cc_start: 0.9198 (t) cc_final: 0.8412 (p) REVERT: C 734 ASP cc_start: 0.8293 (t0) cc_final: 0.7742 (t0) REVERT: C 737 MET cc_start: 0.8722 (tpp) cc_final: 0.8374 (tpt) REVERT: C 762 ARG cc_start: 0.8671 (mtm180) cc_final: 0.8434 (mtm180) REVERT: C 781 GLN cc_start: 0.8586 (mt0) cc_final: 0.7524 (mt0) REVERT: C 803 LEU cc_start: 0.9765 (mt) cc_final: 0.9265 (pp) REVERT: C 853 ASN cc_start: 0.8868 (m-40) cc_final: 0.8658 (m110) REVERT: C 855 LEU cc_start: 0.9238 (mt) cc_final: 0.9017 (mt) REVERT: C 893 ILE cc_start: 0.9287 (tp) cc_final: 0.8973 (tp) REVERT: C 918 LYS cc_start: 0.9666 (mttt) cc_final: 0.9339 (mptt) REVERT: C 947 ASP cc_start: 0.9201 (m-30) cc_final: 0.8862 (p0) REVERT: C 948 VAL cc_start: 0.9333 (t) cc_final: 0.8828 (t) REVERT: C 961 LYS cc_start: 0.9460 (mttt) cc_final: 0.8989 (mmtt) REVERT: C 1001 LEU cc_start: 0.9448 (mt) cc_final: 0.9214 (mt) REVERT: C 1009 LEU cc_start: 0.9621 (mt) cc_final: 0.9409 (mm) REVERT: C 1011 ARG cc_start: 0.9197 (tpp-160) cc_final: 0.8864 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9270 (pt0) cc_final: 0.8804 (pp20) REVERT: C 1026 MET cc_start: 0.9376 (tpt) cc_final: 0.9096 (tpt) REVERT: C 1051 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8325 (tp-100) REVERT: C 1073 THR cc_start: 0.9277 (m) cc_final: 0.8965 (m) REVERT: H 32 TYR cc_start: 0.9205 (m-80) cc_final: 0.8804 (m-80) REVERT: H 34 MET cc_start: 0.2712 (mpp) cc_final: 0.2223 (mpp) REVERT: H 83 MET cc_start: -0.6709 (ptt) cc_final: -0.7023 (ptt) REVERT: H 105 PHE cc_start: 0.6394 (m-10) cc_final: 0.6177 (m-80) REVERT: E 34 MET cc_start: -0.5094 (mmt) cc_final: -0.5336 (mmt) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.4033 time to fit residues: 335.7510 Evaluate side-chains 421 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 369 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 330 optimal weight: 40.0000 chunk 99 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 318 GLN A 577 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN A 761 ASN A 781 GLN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 975 ASN A1020 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN B 761 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN B 869 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN B 950 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 ASN ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN J 35 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 31689 Z= 0.550 Angle : 0.958 16.606 43124 Z= 0.520 Chirality : 0.052 0.287 4983 Planarity : 0.007 0.098 5509 Dihedral : 7.122 56.673 5297 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 35.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.34 % Rotamer: Outliers : 0.54 % Allowed : 5.04 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3827 helix: -2.12 (0.16), residues: 698 sheet: -0.29 (0.16), residues: 963 loop : -1.02 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 90 HIS 0.017 0.003 HIS B1061 PHE 0.042 0.004 PHE B 58 TYR 0.039 0.003 TYR C 738 ARG 0.017 0.001 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 420 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8523 (p) cc_final: 0.7673 (m) REVERT: A 58 PHE cc_start: 0.8744 (m-10) cc_final: 0.8380 (m-10) REVERT: A 420 TYR cc_start: 0.8546 (t80) cc_final: 0.8012 (t80) REVERT: A 453 PHE cc_start: 0.9341 (m-80) cc_final: 0.9051 (m-10) REVERT: A 529 ASN cc_start: 0.9654 (m-40) cc_final: 0.9330 (p0) REVERT: A 759 GLN cc_start: 0.9611 (pt0) cc_final: 0.9384 (pt0) REVERT: A 818 LEU cc_start: 0.9611 (mt) cc_final: 0.9398 (mt) REVERT: A 918 LYS cc_start: 0.9739 (mttt) cc_final: 0.9315 (tppt) REVERT: A 944 LYS cc_start: 0.9448 (mttt) cc_final: 0.9214 (mtmm) REVERT: A 954 GLN cc_start: 0.9592 (mt0) cc_final: 0.9323 (pt0) REVERT: A 957 ASN cc_start: 0.9475 (m110) cc_final: 0.9107 (m110) REVERT: A 958 THR cc_start: 0.9503 (p) cc_final: 0.9237 (p) REVERT: A 961 LYS cc_start: 0.9301 (mttt) cc_final: 0.8823 (mttm) REVERT: A 989 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8813 (mt0) REVERT: A 1001 LEU cc_start: 0.9452 (mt) cc_final: 0.9213 (mt) REVERT: A 1007 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8558 (tm-30) REVERT: A 1049 PHE cc_start: 0.8976 (m-10) cc_final: 0.8774 (m-10) REVERT: B 153 MET cc_start: 0.8690 (tmm) cc_final: 0.8176 (mtp) REVERT: B 177 MET cc_start: 0.1991 (ttm) cc_final: -0.2629 (mmt) REVERT: B 290 LEU cc_start: 0.9344 (tt) cc_final: 0.9137 (mt) REVERT: B 315 PHE cc_start: 0.8628 (t80) cc_final: 0.8331 (t80) REVERT: B 362 TYR cc_start: 0.9578 (m-80) cc_final: 0.9151 (m-80) REVERT: B 384 LEU cc_start: 0.9663 (mm) cc_final: 0.9244 (mt) REVERT: B 551 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9095 (mm-30) REVERT: B 655 ASN cc_start: 0.8565 (m-40) cc_final: 0.7844 (t0) REVERT: B 774 ASN cc_start: 0.8862 (m-40) cc_final: 0.8519 (m110) REVERT: B 781 GLN cc_start: 0.9069 (mm110) cc_final: 0.8867 (mm110) REVERT: B 975 ASN cc_start: 0.9572 (m-40) cc_final: 0.9202 (t0) REVERT: B 989 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8940 (mp10) REVERT: B 1001 LEU cc_start: 0.9343 (mt) cc_final: 0.9104 (mm) REVERT: B 1014 GLU cc_start: 0.9217 (tt0) cc_final: 0.8673 (mm-30) REVERT: B 1100 PHE cc_start: 0.9549 (m-80) cc_final: 0.9292 (m-80) REVERT: C 58 PHE cc_start: 0.9216 (m-10) cc_final: 0.8931 (m-10) REVERT: C 295 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8906 (mm-30) REVERT: C 348 TYR cc_start: 0.9387 (p90) cc_final: 0.9048 (p90) REVERT: C 377 TYR cc_start: 0.8119 (m-80) cc_final: 0.7520 (m-80) REVERT: C 647 LEU cc_start: 0.9180 (tp) cc_final: 0.8813 (pp) REVERT: C 737 MET cc_start: 0.8615 (tpp) cc_final: 0.8362 (tpp) REVERT: C 749 LEU cc_start: 0.9685 (mt) cc_final: 0.9396 (tt) REVERT: C 752 GLN cc_start: 0.8887 (mt0) cc_final: 0.8620 (mt0) REVERT: C 762 ARG cc_start: 0.8910 (mtm180) cc_final: 0.8330 (mtm180) REVERT: C 771 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8598 (mm-40) REVERT: C 781 GLN cc_start: 0.8668 (mt0) cc_final: 0.8369 (mt0) REVERT: C 918 LYS cc_start: 0.9701 (mttt) cc_final: 0.9335 (mptt) REVERT: C 961 LYS cc_start: 0.9477 (mttt) cc_final: 0.8984 (mttt) REVERT: C 1009 LEU cc_start: 0.9631 (mt) cc_final: 0.9410 (mm) REVERT: C 1014 GLU cc_start: 0.9265 (pt0) cc_final: 0.8878 (pp20) REVERT: H 34 MET cc_start: 0.2470 (mpp) cc_final: 0.2039 (mpp) REVERT: H 83 MET cc_start: -0.6141 (ptt) cc_final: -0.6573 (ptt) outliers start: 18 outliers final: 8 residues processed: 434 average time/residue: 0.4061 time to fit residues: 287.7448 Evaluate side-chains 334 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 326 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 274 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 315 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 0.9980 chunk 331 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN A 950 ASN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 774 ASN B 910 GLN B 922 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 385 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 923 GLN C 946 GLN C1007 GLN C1051 GLN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31689 Z= 0.212 Angle : 0.607 14.585 43124 Z= 0.326 Chirality : 0.045 0.260 4983 Planarity : 0.004 0.053 5509 Dihedral : 6.048 59.829 5297 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3827 helix: -0.56 (0.18), residues: 688 sheet: -0.08 (0.16), residues: 936 loop : -0.79 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 34 HIS 0.008 0.001 HIS B1061 PHE 0.033 0.002 PHE A 556 TYR 0.017 0.001 TYR B 263 ARG 0.008 0.001 ARG C 574 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8423 (p) cc_final: 0.7478 (m) REVERT: A 58 PHE cc_start: 0.8625 (m-10) cc_final: 0.8282 (m-10) REVERT: A 377 TYR cc_start: 0.9223 (m-80) cc_final: 0.9020 (m-80) REVERT: A 420 TYR cc_start: 0.8525 (t80) cc_final: 0.7706 (t80) REVERT: A 453 PHE cc_start: 0.9316 (m-80) cc_final: 0.9044 (m-10) REVERT: A 529 ASN cc_start: 0.9695 (m-40) cc_final: 0.9361 (p0) REVERT: A 568 ASP cc_start: 0.9474 (m-30) cc_final: 0.8380 (t0) REVERT: A 592 VAL cc_start: 0.9435 (t) cc_final: 0.9163 (m) REVERT: A 734 ASP cc_start: 0.8452 (t0) cc_final: 0.8143 (t0) REVERT: A 753 TYR cc_start: 0.9421 (m-10) cc_final: 0.8831 (m-10) REVERT: A 756 PHE cc_start: 0.9101 (m-10) cc_final: 0.8762 (m-10) REVERT: A 760 LEU cc_start: 0.9652 (mt) cc_final: 0.8807 (mt) REVERT: A 818 LEU cc_start: 0.9569 (mt) cc_final: 0.9288 (mp) REVERT: A 918 LYS cc_start: 0.9698 (mttt) cc_final: 0.9272 (tppt) REVERT: A 919 LEU cc_start: 0.9384 (mp) cc_final: 0.8842 (mp) REVERT: A 922 ASN cc_start: 0.9659 (m-40) cc_final: 0.8990 (m110) REVERT: A 935 LEU cc_start: 0.9671 (mm) cc_final: 0.9437 (pp) REVERT: A 954 GLN cc_start: 0.9440 (mt0) cc_final: 0.9198 (pt0) REVERT: A 961 LYS cc_start: 0.9148 (mttt) cc_final: 0.8635 (ptpp) REVERT: A 970 ILE cc_start: 0.9026 (pt) cc_final: 0.8625 (pt) REVERT: A 989 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8493 (mt0) REVERT: A 995 THR cc_start: 0.9363 (m) cc_final: 0.8983 (m) REVERT: A 998 LEU cc_start: 0.9744 (tt) cc_final: 0.9483 (pp) REVERT: A 999 GLN cc_start: 0.9216 (mt0) cc_final: 0.8940 (mp10) REVERT: A 1002 GLN cc_start: 0.9610 (tp40) cc_final: 0.9276 (tp-100) REVERT: A 1003 THR cc_start: 0.9581 (m) cc_final: 0.9376 (m) REVERT: B 177 MET cc_start: 0.0984 (ttm) cc_final: -0.2526 (mmt) REVERT: B 290 LEU cc_start: 0.9328 (tt) cc_final: 0.9121 (mt) REVERT: B 362 TYR cc_start: 0.9527 (m-80) cc_final: 0.9116 (m-80) REVERT: B 384 LEU cc_start: 0.9713 (mm) cc_final: 0.9290 (mt) REVERT: B 589 PHE cc_start: 0.8649 (p90) cc_final: 0.8408 (p90) REVERT: B 655 ASN cc_start: 0.8697 (m-40) cc_final: 0.7912 (t0) REVERT: B 694 MET cc_start: 0.8558 (ppp) cc_final: 0.8310 (ppp) REVERT: B 717 ILE cc_start: 0.8510 (mt) cc_final: 0.7881 (mt) REVERT: B 752 GLN cc_start: 0.8440 (mt0) cc_final: 0.8118 (mt0) REVERT: B 781 GLN cc_start: 0.9074 (mm110) cc_final: 0.8689 (tm-30) REVERT: B 803 LEU cc_start: 0.9393 (mt) cc_final: 0.8911 (pp) REVERT: B 916 ASN cc_start: 0.9597 (m-40) cc_final: 0.9336 (p0) REVERT: B 951 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8574 (tp40) REVERT: B 957 ASN cc_start: 0.9328 (m110) cc_final: 0.8876 (m110) REVERT: B 975 ASN cc_start: 0.9604 (m-40) cc_final: 0.9263 (t0) REVERT: B 989 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8858 (mp10) REVERT: B 999 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8959 (tm-30) REVERT: B 1014 GLU cc_start: 0.8986 (tt0) cc_final: 0.8239 (mm-30) REVERT: B 1031 LEU cc_start: 0.8693 (mp) cc_final: 0.8415 (mp) REVERT: B 1100 PHE cc_start: 0.9439 (m-80) cc_final: 0.9237 (m-80) REVERT: C 53 ASP cc_start: 0.9046 (m-30) cc_final: 0.8801 (m-30) REVERT: C 58 PHE cc_start: 0.9170 (m-10) cc_final: 0.8922 (m-10) REVERT: C 177 MET cc_start: 0.3697 (ttm) cc_final: 0.3278 (ttm) REVERT: C 223 LEU cc_start: 0.9205 (mp) cc_final: 0.8945 (mp) REVERT: C 295 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8645 (mm-30) REVERT: C 315 PHE cc_start: 0.7994 (t80) cc_final: 0.7325 (t80) REVERT: C 321 GLU cc_start: 0.9268 (tp30) cc_final: 0.8632 (tp30) REVERT: C 348 TYR cc_start: 0.9288 (p90) cc_final: 0.8969 (p90) REVERT: C 377 TYR cc_start: 0.7825 (m-80) cc_final: 0.7239 (m-80) REVERT: C 612 VAL cc_start: 0.8797 (t) cc_final: 0.8537 (m) REVERT: C 647 LEU cc_start: 0.9228 (tp) cc_final: 0.8974 (pp) REVERT: C 767 ILE cc_start: 0.9826 (mt) cc_final: 0.9560 (mt) REVERT: C 770 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9211 (mt-10) REVERT: C 781 GLN cc_start: 0.8630 (mt0) cc_final: 0.7533 (mt0) REVERT: C 916 ASN cc_start: 0.9480 (m-40) cc_final: 0.9179 (m-40) REVERT: C 918 LYS cc_start: 0.9622 (mttt) cc_final: 0.9194 (mptt) REVERT: C 947 ASP cc_start: 0.9189 (m-30) cc_final: 0.8953 (p0) REVERT: C 948 VAL cc_start: 0.9379 (t) cc_final: 0.8917 (t) REVERT: C 961 LYS cc_start: 0.9292 (mttt) cc_final: 0.8880 (mmtt) REVERT: C 999 GLN cc_start: 0.9289 (mp10) cc_final: 0.9011 (mp10) REVERT: C 1011 ARG cc_start: 0.9141 (tpp-160) cc_final: 0.8664 (tpp-160) REVERT: C 1021 LEU cc_start: 0.9501 (mt) cc_final: 0.9288 (mt) REVERT: C 1026 MET cc_start: 0.9394 (tpt) cc_final: 0.9184 (tpt) REVERT: C 1028 GLU cc_start: 0.9164 (tp30) cc_final: 0.8684 (tp30) REVERT: C 1031 LEU cc_start: 0.9535 (mp) cc_final: 0.9173 (mp) REVERT: H 32 TYR cc_start: 0.9260 (m-80) cc_final: 0.8919 (m-80) REVERT: H 34 MET cc_start: 0.2537 (mpp) cc_final: 0.2072 (mpp) REVERT: H 83 MET cc_start: -0.6450 (ptt) cc_final: -0.6725 (ptt) REVERT: H 105 PHE cc_start: 0.6585 (m-10) cc_final: 0.6139 (m-80) REVERT: E 73 ASP cc_start: 0.5004 (m-30) cc_final: 0.4554 (p0) outliers start: 1 outliers final: 1 residues processed: 469 average time/residue: 0.4054 time to fit residues: 312.6796 Evaluate side-chains 364 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.9990 chunk 332 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 369 optimal weight: 50.0000 chunk 306 optimal weight: 0.4980 chunk 171 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 ASN ** C 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31689 Z= 0.230 Angle : 0.596 13.568 43124 Z= 0.320 Chirality : 0.044 0.235 4983 Planarity : 0.004 0.096 5509 Dihedral : 5.683 53.066 5297 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3827 helix: -0.25 (0.19), residues: 684 sheet: -0.09 (0.16), residues: 975 loop : -0.71 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.016 0.001 HIS B1045 PHE 0.027 0.002 PHE C 272 TYR 0.027 0.001 TYR B 263 ARG 0.010 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8399 (p) cc_final: 0.7520 (m) REVERT: A 58 PHE cc_start: 0.8611 (m-10) cc_final: 0.8272 (m-10) REVERT: A 377 TYR cc_start: 0.9273 (m-80) cc_final: 0.8975 (m-80) REVERT: A 420 TYR cc_start: 0.8259 (t80) cc_final: 0.7547 (t80) REVERT: A 453 PHE cc_start: 0.9330 (m-80) cc_final: 0.9061 (m-10) REVERT: A 529 ASN cc_start: 0.9668 (m-40) cc_final: 0.9352 (p0) REVERT: A 568 ASP cc_start: 0.9767 (m-30) cc_final: 0.9225 (t0) REVERT: A 737 MET cc_start: 0.8914 (tpp) cc_final: 0.8643 (tpp) REVERT: A 753 TYR cc_start: 0.9323 (m-10) cc_final: 0.8872 (m-10) REVERT: A 756 PHE cc_start: 0.9131 (m-10) cc_final: 0.8906 (m-10) REVERT: A 759 GLN cc_start: 0.9353 (pp30) cc_final: 0.9121 (pp30) REVERT: A 760 LEU cc_start: 0.9358 (mt) cc_final: 0.8988 (mt) REVERT: A 897 MET cc_start: 0.7396 (mpp) cc_final: 0.7083 (mpp) REVERT: A 918 LYS cc_start: 0.9686 (mttt) cc_final: 0.9317 (tppt) REVERT: A 954 GLN cc_start: 0.9503 (mt0) cc_final: 0.9281 (pt0) REVERT: A 957 ASN cc_start: 0.9329 (m110) cc_final: 0.8811 (m110) REVERT: A 958 THR cc_start: 0.9541 (p) cc_final: 0.9242 (p) REVERT: A 961 LYS cc_start: 0.9157 (mttt) cc_final: 0.8705 (mttm) REVERT: A 963 LEU cc_start: 0.9371 (mt) cc_final: 0.8961 (tt) REVERT: A 970 ILE cc_start: 0.8990 (pt) cc_final: 0.8702 (pt) REVERT: A 977 ILE cc_start: 0.9651 (pt) cc_final: 0.9431 (pt) REVERT: A 989 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8680 (mt0) REVERT: A 994 ILE cc_start: 0.8918 (mt) cc_final: 0.8691 (mt) REVERT: A 1002 GLN cc_start: 0.9602 (tp40) cc_final: 0.9221 (tp-100) REVERT: B 177 MET cc_start: 0.0685 (ttm) cc_final: -0.2514 (mmt) REVERT: B 315 PHE cc_start: 0.8523 (t80) cc_final: 0.8302 (t80) REVERT: B 362 TYR cc_start: 0.9540 (m-80) cc_final: 0.9139 (m-80) REVERT: B 384 LEU cc_start: 0.9725 (mm) cc_final: 0.9289 (mt) REVERT: B 589 PHE cc_start: 0.8399 (p90) cc_final: 0.8128 (p90) REVERT: B 655 ASN cc_start: 0.8675 (m-40) cc_final: 0.8008 (t0) REVERT: B 694 MET cc_start: 0.8553 (ppp) cc_final: 0.8331 (ppp) REVERT: B 717 ILE cc_start: 0.8529 (mt) cc_final: 0.7936 (mt) REVERT: B 752 GLN cc_start: 0.8488 (mt0) cc_final: 0.8142 (mt0) REVERT: B 769 VAL cc_start: 0.9418 (t) cc_final: 0.9056 (p) REVERT: B 781 GLN cc_start: 0.9086 (mm110) cc_final: 0.8697 (tm-30) REVERT: B 803 LEU cc_start: 0.9409 (mt) cc_final: 0.8937 (pp) REVERT: B 903 PHE cc_start: 0.8019 (m-10) cc_final: 0.7676 (m-10) REVERT: B 951 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8526 (tp40) REVERT: B 957 ASN cc_start: 0.9283 (m110) cc_final: 0.8834 (m110) REVERT: B 975 ASN cc_start: 0.9625 (m-40) cc_final: 0.9295 (t0) REVERT: B 989 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8874 (mp10) REVERT: B 999 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9001 (tm-30) REVERT: B 1014 GLU cc_start: 0.8942 (tt0) cc_final: 0.8213 (mm-30) REVERT: B 1031 LEU cc_start: 0.8714 (mp) cc_final: 0.8446 (mp) REVERT: B 1051 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8041 (mt0) REVERT: B 1100 PHE cc_start: 0.9483 (m-80) cc_final: 0.9260 (m-80) REVERT: C 58 PHE cc_start: 0.9240 (m-10) cc_final: 0.8782 (m-10) REVERT: C 177 MET cc_start: 0.3840 (ttm) cc_final: 0.3386 (ttm) REVERT: C 189 LEU cc_start: 0.9525 (tp) cc_final: 0.8689 (tp) REVERT: C 191 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8321 (mp0) REVERT: C 223 LEU cc_start: 0.9235 (mp) cc_final: 0.8929 (mp) REVERT: C 295 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 315 PHE cc_start: 0.7752 (t80) cc_final: 0.7129 (t80) REVERT: C 321 GLU cc_start: 0.9293 (tp30) cc_final: 0.8737 (tp30) REVERT: C 348 TYR cc_start: 0.9244 (p90) cc_final: 0.8914 (p90) REVERT: C 377 TYR cc_start: 0.7817 (m-80) cc_final: 0.7234 (m-80) REVERT: C 612 VAL cc_start: 0.8941 (t) cc_final: 0.8708 (m) REVERT: C 647 LEU cc_start: 0.9208 (tp) cc_final: 0.8860 (pp) REVERT: C 728 MET cc_start: 0.9354 (ptm) cc_final: 0.8933 (ptm) REVERT: C 762 ARG cc_start: 0.8895 (mtm180) cc_final: 0.8645 (mtm180) REVERT: C 770 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9244 (mt-10) REVERT: C 781 GLN cc_start: 0.8666 (mt0) cc_final: 0.7675 (mt0) REVERT: C 916 ASN cc_start: 0.9470 (m-40) cc_final: 0.9168 (m-40) REVERT: C 918 LYS cc_start: 0.9658 (mttt) cc_final: 0.9260 (mptt) REVERT: C 947 ASP cc_start: 0.9221 (m-30) cc_final: 0.8922 (p0) REVERT: C 948 VAL cc_start: 0.9343 (t) cc_final: 0.8920 (t) REVERT: C 957 ASN cc_start: 0.9477 (m110) cc_final: 0.9038 (m110) REVERT: C 961 LYS cc_start: 0.9307 (mttt) cc_final: 0.8829 (mttt) REVERT: C 999 GLN cc_start: 0.9286 (mp10) cc_final: 0.9037 (mp10) REVERT: C 1009 LEU cc_start: 0.9409 (mm) cc_final: 0.9189 (mm) REVERT: C 1011 ARG cc_start: 0.9193 (tpp-160) cc_final: 0.8689 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9145 (pt0) cc_final: 0.8766 (pp20) REVERT: C 1026 MET cc_start: 0.9362 (tpt) cc_final: 0.9140 (tpt) REVERT: C 1051 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8308 (tp-100) REVERT: H 32 TYR cc_start: 0.9378 (m-80) cc_final: 0.9132 (m-80) REVERT: H 34 MET cc_start: 0.2558 (mpp) cc_final: 0.2097 (mpp) REVERT: H 83 MET cc_start: -0.6305 (ptt) cc_final: -0.6677 (ptt) REVERT: H 105 PHE cc_start: 0.6445 (m-10) cc_final: 0.6237 (m-80) REVERT: E 19 ARG cc_start: 0.6233 (mmt90) cc_final: 0.5973 (mmt180) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.3968 time to fit residues: 286.9825 Evaluate side-chains 359 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 269 optimal weight: 0.3980 chunk 209 optimal weight: 0.9990 chunk 311 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 368 optimal weight: 40.0000 chunk 230 optimal weight: 0.4980 chunk 224 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 946 GLN A 950 ASN A 975 ASN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31689 Z= 0.167 Angle : 0.549 13.341 43124 Z= 0.291 Chirality : 0.044 0.224 4983 Planarity : 0.004 0.047 5509 Dihedral : 5.172 49.739 5297 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3827 helix: 0.41 (0.19), residues: 683 sheet: 0.06 (0.16), residues: 1009 loop : -0.67 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 34 HIS 0.009 0.001 HIS B1045 PHE 0.027 0.002 PHE C 272 TYR 0.028 0.001 TYR A 901 ARG 0.014 0.000 ARG C 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8368 (p) cc_final: 0.7491 (m) REVERT: A 58 PHE cc_start: 0.8628 (m-10) cc_final: 0.8311 (m-10) REVERT: A 314 ASN cc_start: 0.9047 (m-40) cc_final: 0.8645 (t0) REVERT: A 377 TYR cc_start: 0.9395 (m-80) cc_final: 0.9078 (m-80) REVERT: A 420 TYR cc_start: 0.8546 (t80) cc_final: 0.7713 (t80) REVERT: A 453 PHE cc_start: 0.9325 (m-80) cc_final: 0.9061 (m-10) REVERT: A 529 ASN cc_start: 0.9643 (m-40) cc_final: 0.9325 (p0) REVERT: A 568 ASP cc_start: 0.9756 (m-30) cc_final: 0.9127 (t0) REVERT: A 737 MET cc_start: 0.9011 (tpp) cc_final: 0.8637 (tpp) REVERT: A 756 PHE cc_start: 0.9237 (m-10) cc_final: 0.8954 (m-80) REVERT: A 759 GLN cc_start: 0.9371 (pp30) cc_final: 0.9071 (pp30) REVERT: A 760 LEU cc_start: 0.9411 (mt) cc_final: 0.8926 (mt) REVERT: A 773 LYS cc_start: 0.9621 (mttm) cc_final: 0.9341 (mtpp) REVERT: A 805 ASP cc_start: 0.7656 (t0) cc_final: 0.7278 (p0) REVERT: A 818 LEU cc_start: 0.9545 (mm) cc_final: 0.9097 (mp) REVERT: A 918 LYS cc_start: 0.9623 (mttt) cc_final: 0.9208 (tppt) REVERT: A 922 ASN cc_start: 0.9450 (m-40) cc_final: 0.8759 (m110) REVERT: A 954 GLN cc_start: 0.9367 (mt0) cc_final: 0.9133 (pt0) REVERT: A 957 ASN cc_start: 0.9301 (m110) cc_final: 0.8986 (m-40) REVERT: A 970 ILE cc_start: 0.9029 (pt) cc_final: 0.8710 (pt) REVERT: A 977 ILE cc_start: 0.9612 (pt) cc_final: 0.9404 (pt) REVERT: A 989 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8622 (mt0) REVERT: A 998 LEU cc_start: 0.9807 (tt) cc_final: 0.9521 (pp) REVERT: A 999 GLN cc_start: 0.9367 (mp10) cc_final: 0.8825 (mp10) REVERT: A 1001 LEU cc_start: 0.9412 (mt) cc_final: 0.9174 (mt) REVERT: A 1002 GLN cc_start: 0.9547 (tp40) cc_final: 0.9083 (tp-100) REVERT: B 177 MET cc_start: 0.0637 (ttm) cc_final: -0.2993 (mmt) REVERT: B 204 TYR cc_start: 0.5779 (m-10) cc_final: 0.5515 (m-10) REVERT: B 315 PHE cc_start: 0.8492 (t80) cc_final: 0.8267 (t80) REVERT: B 362 TYR cc_start: 0.9458 (m-80) cc_final: 0.9055 (m-80) REVERT: B 384 LEU cc_start: 0.9733 (mm) cc_final: 0.9308 (mt) REVERT: B 589 PHE cc_start: 0.8419 (p90) cc_final: 0.7931 (p90) REVERT: B 694 MET cc_start: 0.8465 (ppp) cc_final: 0.8241 (ppp) REVERT: B 717 ILE cc_start: 0.8502 (mt) cc_final: 0.7888 (mt) REVERT: B 774 ASN cc_start: 0.8860 (m110) cc_final: 0.8523 (m110) REVERT: B 781 GLN cc_start: 0.9029 (mm110) cc_final: 0.8612 (tm-30) REVERT: B 803 LEU cc_start: 0.9390 (mt) cc_final: 0.8916 (pp) REVERT: B 903 PHE cc_start: 0.8325 (m-10) cc_final: 0.8070 (m-10) REVERT: B 951 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8762 (tp40) REVERT: B 952 ASN cc_start: 0.9479 (t0) cc_final: 0.9255 (t0) REVERT: B 956 LEU cc_start: 0.9747 (mt) cc_final: 0.9537 (mt) REVERT: B 957 ASN cc_start: 0.9419 (m110) cc_final: 0.9058 (m-40) REVERT: B 975 ASN cc_start: 0.9665 (m-40) cc_final: 0.9375 (t0) REVERT: B 989 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8638 (mp10) REVERT: B 1014 GLU cc_start: 0.8812 (tt0) cc_final: 0.8144 (mm-30) REVERT: B 1051 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8160 (mt0) REVERT: C 53 ASP cc_start: 0.9281 (m-30) cc_final: 0.8941 (m-30) REVERT: C 58 PHE cc_start: 0.9157 (m-10) cc_final: 0.8840 (m-80) REVERT: C 153 MET cc_start: 0.9099 (ptp) cc_final: 0.8890 (pmm) REVERT: C 177 MET cc_start: 0.3420 (ttm) cc_final: 0.2947 (ttm) REVERT: C 223 LEU cc_start: 0.9199 (mp) cc_final: 0.8965 (mp) REVERT: C 321 GLU cc_start: 0.9233 (tp30) cc_final: 0.8633 (tp30) REVERT: C 348 TYR cc_start: 0.9259 (p90) cc_final: 0.8974 (p90) REVERT: C 377 TYR cc_start: 0.7756 (m-80) cc_final: 0.7019 (m-80) REVERT: C 647 LEU cc_start: 0.9230 (tp) cc_final: 0.8797 (pp) REVERT: C 728 MET cc_start: 0.9262 (ptm) cc_final: 0.9019 (ptm) REVERT: C 781 GLN cc_start: 0.8603 (mt0) cc_final: 0.8186 (mt0) REVERT: C 916 ASN cc_start: 0.9416 (m-40) cc_final: 0.9087 (m-40) REVERT: C 918 LYS cc_start: 0.9636 (mttt) cc_final: 0.9217 (mptt) REVERT: C 948 VAL cc_start: 0.9398 (t) cc_final: 0.9026 (t) REVERT: C 957 ASN cc_start: 0.9463 (m110) cc_final: 0.9220 (m110) REVERT: C 961 LYS cc_start: 0.9212 (mttt) cc_final: 0.8749 (mmtt) REVERT: C 989 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8391 (mm-40) REVERT: C 1009 LEU cc_start: 0.9418 (mm) cc_final: 0.9106 (mm) REVERT: C 1011 ARG cc_start: 0.9161 (tpp-160) cc_final: 0.8691 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9108 (pt0) cc_final: 0.8739 (pp20) REVERT: H 32 TYR cc_start: 0.9347 (m-80) cc_final: 0.9091 (m-80) REVERT: H 34 MET cc_start: 0.2641 (mpp) cc_final: 0.2174 (mpp) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.3902 time to fit residues: 294.7765 Evaluate side-chains 367 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 72 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 946 GLN A 950 ASN A 975 ASN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31689 Z= 0.243 Angle : 0.599 12.982 43124 Z= 0.321 Chirality : 0.044 0.214 4983 Planarity : 0.004 0.045 5509 Dihedral : 5.238 49.424 5297 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3827 helix: 0.10 (0.19), residues: 678 sheet: 0.06 (0.16), residues: 966 loop : -0.67 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.010 0.001 HIS B1045 PHE 0.026 0.002 PHE C 272 TYR 0.026 0.001 TYR A 738 ARG 0.007 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8345 (p) cc_final: 0.7504 (m) REVERT: A 58 PHE cc_start: 0.8686 (m-10) cc_final: 0.8358 (m-10) REVERT: A 314 ASN cc_start: 0.9115 (m-40) cc_final: 0.8723 (t0) REVERT: A 325 ARG cc_start: 0.7946 (mmp-170) cc_final: 0.5383 (tpp-160) REVERT: A 377 TYR cc_start: 0.9418 (m-80) cc_final: 0.9059 (m-80) REVERT: A 420 TYR cc_start: 0.8328 (t80) cc_final: 0.7639 (t80) REVERT: A 453 PHE cc_start: 0.9353 (m-80) cc_final: 0.9094 (m-10) REVERT: A 529 ASN cc_start: 0.9665 (m-40) cc_final: 0.9028 (p0) REVERT: A 568 ASP cc_start: 0.9752 (m-30) cc_final: 0.9153 (t0) REVERT: A 734 ASP cc_start: 0.8714 (t0) cc_final: 0.8365 (t0) REVERT: A 737 MET cc_start: 0.9046 (tpp) cc_final: 0.8685 (tpp) REVERT: A 748 ASN cc_start: 0.8653 (t0) cc_final: 0.8423 (t0) REVERT: A 753 TYR cc_start: 0.9424 (m-10) cc_final: 0.9124 (m-10) REVERT: A 756 PHE cc_start: 0.9250 (m-10) cc_final: 0.9019 (m-10) REVERT: A 760 LEU cc_start: 0.9425 (mt) cc_final: 0.9017 (mt) REVERT: A 773 LYS cc_start: 0.9642 (mttm) cc_final: 0.9440 (mtpp) REVERT: A 818 LEU cc_start: 0.9546 (mm) cc_final: 0.9332 (mp) REVERT: A 897 MET cc_start: 0.7376 (mpp) cc_final: 0.7118 (mpp) REVERT: A 918 LYS cc_start: 0.9667 (mttt) cc_final: 0.9228 (tppt) REVERT: A 922 ASN cc_start: 0.9501 (m-40) cc_final: 0.8817 (m110) REVERT: A 954 GLN cc_start: 0.9406 (mt0) cc_final: 0.9146 (pt0) REVERT: A 957 ASN cc_start: 0.9309 (m110) cc_final: 0.8981 (m-40) REVERT: A 989 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8252 (mp10) REVERT: A 999 GLN cc_start: 0.9368 (mp10) cc_final: 0.8975 (mp10) REVERT: A 1001 LEU cc_start: 0.9459 (mt) cc_final: 0.9230 (mt) REVERT: A 1002 GLN cc_start: 0.9506 (tp40) cc_final: 0.9090 (tp-100) REVERT: B 153 MET cc_start: 0.7327 (pmm) cc_final: 0.7049 (pmm) REVERT: B 177 MET cc_start: 0.0810 (ttm) cc_final: -0.2128 (mmt) REVERT: B 315 PHE cc_start: 0.8506 (t80) cc_final: 0.8272 (t80) REVERT: B 362 TYR cc_start: 0.9497 (m-80) cc_final: 0.9091 (m-80) REVERT: B 384 LEU cc_start: 0.9756 (mm) cc_final: 0.9323 (mt) REVERT: B 589 PHE cc_start: 0.8358 (p90) cc_final: 0.8053 (p90) REVERT: B 694 MET cc_start: 0.8535 (ppp) cc_final: 0.8223 (ppp) REVERT: B 717 ILE cc_start: 0.8551 (mt) cc_final: 0.7964 (mt) REVERT: B 752 GLN cc_start: 0.8638 (mt0) cc_final: 0.8294 (mt0) REVERT: B 774 ASN cc_start: 0.8746 (m110) cc_final: 0.8459 (m110) REVERT: B 803 LEU cc_start: 0.9426 (mt) cc_final: 0.8944 (pp) REVERT: B 903 PHE cc_start: 0.8063 (m-10) cc_final: 0.7708 (m-10) REVERT: B 951 GLN cc_start: 0.9270 (tp-100) cc_final: 0.8771 (tp40) REVERT: B 952 ASN cc_start: 0.9552 (t0) cc_final: 0.9346 (m110) REVERT: B 957 ASN cc_start: 0.9315 (m110) cc_final: 0.8941 (m110) REVERT: B 975 ASN cc_start: 0.9695 (m-40) cc_final: 0.9420 (t0) REVERT: B 989 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8737 (mp10) REVERT: B 1014 GLU cc_start: 0.8974 (tt0) cc_final: 0.8230 (mm-30) REVERT: B 1051 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8090 (mt0) REVERT: B 1100 PHE cc_start: 0.9501 (m-80) cc_final: 0.9244 (m-80) REVERT: C 153 MET cc_start: 0.9194 (ptp) cc_final: 0.8941 (pmm) REVERT: C 177 MET cc_start: 0.3938 (ttm) cc_final: 0.3478 (ttm) REVERT: C 201 PHE cc_start: 0.8658 (t80) cc_final: 0.8416 (t80) REVERT: C 223 LEU cc_start: 0.9168 (mp) cc_final: 0.8945 (mp) REVERT: C 287 ASP cc_start: 0.7727 (t0) cc_final: 0.6930 (t0) REVERT: C 321 GLU cc_start: 0.9312 (tp30) cc_final: 0.8652 (tp30) REVERT: C 348 TYR cc_start: 0.9294 (p90) cc_final: 0.9014 (p90) REVERT: C 377 TYR cc_start: 0.7818 (m-80) cc_final: 0.7223 (m-80) REVERT: C 647 LEU cc_start: 0.9116 (tp) cc_final: 0.8539 (pp) REVERT: C 728 MET cc_start: 0.9419 (ptm) cc_final: 0.9111 (ptm) REVERT: C 781 GLN cc_start: 0.8635 (mt0) cc_final: 0.7564 (mt0) REVERT: C 816 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8913 (mt-10) REVERT: C 866 MET cc_start: 0.9648 (mpp) cc_final: 0.9132 (mtt) REVERT: C 916 ASN cc_start: 0.9430 (m-40) cc_final: 0.9084 (m-40) REVERT: C 918 LYS cc_start: 0.9656 (mttt) cc_final: 0.9259 (mptt) REVERT: C 957 ASN cc_start: 0.9496 (m110) cc_final: 0.9232 (m110) REVERT: C 961 LYS cc_start: 0.9250 (mttt) cc_final: 0.8804 (mmtt) REVERT: C 989 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8488 (mm110) REVERT: C 1009 LEU cc_start: 0.9416 (mm) cc_final: 0.9104 (mm) REVERT: C 1011 ARG cc_start: 0.9203 (tpp-160) cc_final: 0.8869 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9133 (pt0) cc_final: 0.8804 (pp20) REVERT: C 1051 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8379 (mm110) REVERT: H 32 TYR cc_start: 0.9343 (m-80) cc_final: 0.9092 (m-80) REVERT: H 34 MET cc_start: 0.2720 (mpp) cc_final: 0.2209 (mpp) REVERT: H 83 MET cc_start: -0.6045 (ptt) cc_final: -0.6566 (ptt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3900 time to fit residues: 283.3194 Evaluate side-chains 358 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 50.0000 chunk 352 optimal weight: 0.5980 chunk 321 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 310 optimal weight: 0.4980 chunk 324 optimal weight: 40.0000 chunk 341 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31689 Z= 0.268 Angle : 0.637 12.692 43124 Z= 0.342 Chirality : 0.045 0.210 4983 Planarity : 0.004 0.050 5509 Dihedral : 5.467 53.429 5297 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 3827 helix: -0.28 (0.19), residues: 679 sheet: -0.04 (0.16), residues: 955 loop : -0.70 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 34 HIS 0.010 0.001 HIS B1045 PHE 0.027 0.002 PHE C 272 TYR 0.024 0.001 TYR A 738 ARG 0.009 0.001 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8232 (p) cc_final: 0.7395 (m) REVERT: A 58 PHE cc_start: 0.8848 (m-10) cc_final: 0.8593 (m-10) REVERT: A 153 MET cc_start: 0.7931 (pmm) cc_final: 0.7719 (pmm) REVERT: A 295 GLU cc_start: 0.9346 (mp0) cc_final: 0.8703 (mp0) REVERT: A 314 ASN cc_start: 0.9096 (m-40) cc_final: 0.8761 (t0) REVERT: A 377 TYR cc_start: 0.9414 (m-80) cc_final: 0.8783 (m-80) REVERT: A 420 TYR cc_start: 0.8537 (t80) cc_final: 0.7614 (t80) REVERT: A 453 PHE cc_start: 0.9389 (m-80) cc_final: 0.9125 (m-10) REVERT: A 529 ASN cc_start: 0.9674 (m-40) cc_final: 0.9347 (p0) REVERT: A 568 ASP cc_start: 0.9738 (m-30) cc_final: 0.9010 (t0) REVERT: A 737 MET cc_start: 0.9075 (tpp) cc_final: 0.8735 (tpp) REVERT: A 748 ASN cc_start: 0.8487 (t0) cc_final: 0.8269 (t0) REVERT: A 753 TYR cc_start: 0.9670 (m-10) cc_final: 0.9430 (m-10) REVERT: A 760 LEU cc_start: 0.9434 (mt) cc_final: 0.9208 (mt) REVERT: A 773 LYS cc_start: 0.9645 (mttm) cc_final: 0.9400 (mtpp) REVERT: A 897 MET cc_start: 0.6907 (mpp) cc_final: 0.6668 (mpp) REVERT: A 918 LYS cc_start: 0.9691 (mttt) cc_final: 0.9317 (tppt) REVERT: A 954 GLN cc_start: 0.9413 (mt0) cc_final: 0.8998 (pt0) REVERT: A 957 ASN cc_start: 0.9292 (m110) cc_final: 0.8800 (m110) REVERT: A 958 THR cc_start: 0.9575 (p) cc_final: 0.9254 (p) REVERT: A 961 LYS cc_start: 0.9259 (mttt) cc_final: 0.8796 (mttm) REVERT: A 989 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8461 (mp10) REVERT: A 999 GLN cc_start: 0.9330 (mp10) cc_final: 0.8924 (mp10) REVERT: A 1049 PHE cc_start: 0.8947 (m-10) cc_final: 0.8738 (m-10) REVERT: B 118 LEU cc_start: 0.9618 (tt) cc_final: 0.9378 (tp) REVERT: B 153 MET cc_start: 0.7486 (pmm) cc_final: 0.7183 (pmm) REVERT: B 177 MET cc_start: 0.1535 (ttm) cc_final: -0.1486 (mmt) REVERT: B 315 PHE cc_start: 0.8519 (t80) cc_final: 0.8270 (t80) REVERT: B 362 TYR cc_start: 0.9500 (m-80) cc_final: 0.9116 (m-80) REVERT: B 384 LEU cc_start: 0.9765 (mm) cc_final: 0.9326 (mt) REVERT: B 589 PHE cc_start: 0.8378 (p90) cc_final: 0.7990 (p90) REVERT: B 694 MET cc_start: 0.8563 (ppp) cc_final: 0.8284 (ppp) REVERT: B 752 GLN cc_start: 0.8828 (mt0) cc_final: 0.8569 (mt0) REVERT: B 773 LYS cc_start: 0.9265 (pttt) cc_final: 0.8688 (tppt) REVERT: B 774 ASN cc_start: 0.8841 (m110) cc_final: 0.8529 (m110) REVERT: B 903 PHE cc_start: 0.8092 (m-10) cc_final: 0.7692 (m-10) REVERT: B 951 GLN cc_start: 0.9233 (tp-100) cc_final: 0.9016 (tp40) REVERT: B 952 ASN cc_start: 0.9576 (t0) cc_final: 0.9355 (m110) REVERT: B 954 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8213 (pt0) REVERT: B 957 ASN cc_start: 0.9291 (m110) cc_final: 0.9073 (m110) REVERT: B 975 ASN cc_start: 0.9696 (m-40) cc_final: 0.9435 (t0) REVERT: B 989 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8768 (mp10) REVERT: B 1014 GLU cc_start: 0.9007 (tt0) cc_final: 0.8240 (mm-30) REVERT: B 1100 PHE cc_start: 0.9388 (m-80) cc_final: 0.9172 (m-80) REVERT: C 53 ASP cc_start: 0.8788 (m-30) cc_final: 0.8586 (m-30) REVERT: C 58 PHE cc_start: 0.9282 (m-10) cc_final: 0.8931 (m-10) REVERT: C 153 MET cc_start: 0.9226 (ptp) cc_final: 0.8691 (pmm) REVERT: C 223 LEU cc_start: 0.9112 (mp) cc_final: 0.8883 (mp) REVERT: C 321 GLU cc_start: 0.9387 (tp30) cc_final: 0.8813 (tp30) REVERT: C 348 TYR cc_start: 0.9282 (p90) cc_final: 0.9015 (p90) REVERT: C 377 TYR cc_start: 0.7850 (m-80) cc_final: 0.7289 (m-80) REVERT: C 647 LEU cc_start: 0.9122 (tp) cc_final: 0.8554 (pp) REVERT: C 728 MET cc_start: 0.9482 (ptm) cc_final: 0.9218 (ptm) REVERT: C 781 GLN cc_start: 0.8728 (mt0) cc_final: 0.8277 (mt0) REVERT: C 799 PHE cc_start: 0.9047 (m-10) cc_final: 0.8842 (m-10) REVERT: C 816 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8645 (mt-10) REVERT: C 916 ASN cc_start: 0.9475 (m-40) cc_final: 0.9168 (m-40) REVERT: C 918 LYS cc_start: 0.9664 (mttt) cc_final: 0.9254 (mptt) REVERT: C 957 ASN cc_start: 0.9498 (m110) cc_final: 0.9065 (m110) REVERT: C 961 LYS cc_start: 0.9264 (mttt) cc_final: 0.8761 (mttt) REVERT: C 989 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8636 (mm110) REVERT: C 999 GLN cc_start: 0.9260 (mp10) cc_final: 0.8876 (mp10) REVERT: C 1011 ARG cc_start: 0.9323 (tpp-160) cc_final: 0.9031 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9179 (pt0) cc_final: 0.8788 (pp20) REVERT: C 1051 GLN cc_start: 0.8634 (tp-100) cc_final: 0.7870 (mm-40) REVERT: C 1064 TYR cc_start: 0.8337 (t80) cc_final: 0.7912 (t80) REVERT: H 32 TYR cc_start: 0.9348 (m-80) cc_final: 0.9099 (m-80) REVERT: H 34 MET cc_start: 0.2794 (mpp) cc_final: 0.2272 (mpp) REVERT: H 83 MET cc_start: -0.5937 (ptt) cc_final: -0.6711 (ptt) REVERT: E 34 MET cc_start: -0.4261 (tpt) cc_final: -0.4581 (tmm) REVERT: E 73 ASP cc_start: 0.5122 (m-30) cc_final: 0.4540 (p0) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.3871 time to fit residues: 276.9645 Evaluate side-chains 356 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 10.0000 chunk 362 optimal weight: 50.0000 chunk 221 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 chunk 380 optimal weight: 40.0000 chunk 350 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS A 655 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 801 GLN B 946 GLN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 31689 Z= 0.413 Angle : 0.781 13.288 43124 Z= 0.426 Chirality : 0.048 0.243 4983 Planarity : 0.005 0.068 5509 Dihedral : 6.202 58.024 5297 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3827 helix: -1.40 (0.18), residues: 681 sheet: -0.31 (0.16), residues: 969 loop : -0.93 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 883 HIS 0.015 0.002 HIS C1061 PHE 0.031 0.003 PHE A 797 TYR 0.054 0.002 TYR A 738 ARG 0.008 0.001 ARG C 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8313 (p) cc_final: 0.7236 (m) REVERT: A 58 PHE cc_start: 0.8689 (m-10) cc_final: 0.8431 (m-80) REVERT: A 325 ARG cc_start: 0.8070 (mmp-170) cc_final: 0.7271 (tpp-160) REVERT: A 420 TYR cc_start: 0.8640 (t80) cc_final: 0.7763 (t80) REVERT: A 453 PHE cc_start: 0.9333 (m-80) cc_final: 0.9068 (m-10) REVERT: A 529 ASN cc_start: 0.9707 (m-40) cc_final: 0.9263 (p0) REVERT: A 568 ASP cc_start: 0.9754 (m-30) cc_final: 0.9158 (t0) REVERT: A 737 MET cc_start: 0.8937 (tpp) cc_final: 0.8496 (tpp) REVERT: A 748 ASN cc_start: 0.8559 (t0) cc_final: 0.8298 (t0) REVERT: A 918 LYS cc_start: 0.9747 (mttt) cc_final: 0.9415 (tptp) REVERT: A 922 ASN cc_start: 0.9595 (m-40) cc_final: 0.9112 (m-40) REVERT: A 954 GLN cc_start: 0.9507 (mt0) cc_final: 0.9243 (pt0) REVERT: A 957 ASN cc_start: 0.9319 (m110) cc_final: 0.8912 (m110) REVERT: A 958 THR cc_start: 0.9556 (p) cc_final: 0.9347 (p) REVERT: A 961 LYS cc_start: 0.9310 (mttt) cc_final: 0.8889 (mttm) REVERT: A 989 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8546 (mp10) REVERT: A 999 GLN cc_start: 0.9350 (mp10) cc_final: 0.9095 (mp10) REVERT: B 58 PHE cc_start: 0.8772 (m-80) cc_final: 0.8284 (m-80) REVERT: B 118 LEU cc_start: 0.9682 (tt) cc_final: 0.9468 (tp) REVERT: B 177 MET cc_start: 0.0728 (ttm) cc_final: -0.1846 (mmt) REVERT: B 362 TYR cc_start: 0.9505 (m-80) cc_final: 0.9160 (m-80) REVERT: B 384 LEU cc_start: 0.9719 (mm) cc_final: 0.9282 (mt) REVERT: B 589 PHE cc_start: 0.8264 (p90) cc_final: 0.7818 (p90) REVERT: B 694 MET cc_start: 0.8583 (ppp) cc_final: 0.8233 (ppp) REVERT: B 752 GLN cc_start: 0.8773 (mt0) cc_final: 0.8566 (mt0) REVERT: B 774 ASN cc_start: 0.8750 (m110) cc_final: 0.8327 (m110) REVERT: B 951 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8964 (tp40) REVERT: B 952 ASN cc_start: 0.9593 (t0) cc_final: 0.9378 (m110) REVERT: B 954 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8292 (pt0) REVERT: B 957 ASN cc_start: 0.9434 (m110) cc_final: 0.9207 (m110) REVERT: B 975 ASN cc_start: 0.9650 (m-40) cc_final: 0.9384 (t0) REVERT: B 989 GLN cc_start: 0.9421 (mm-40) cc_final: 0.8785 (mp10) REVERT: B 1014 GLU cc_start: 0.9070 (tt0) cc_final: 0.8327 (mm-30) REVERT: B 1051 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8242 (mt0) REVERT: C 58 PHE cc_start: 0.9242 (m-10) cc_final: 0.8955 (m-10) REVERT: C 153 MET cc_start: 0.9372 (ptp) cc_final: 0.8788 (pmm) REVERT: C 201 PHE cc_start: 0.8974 (t80) cc_final: 0.8595 (t80) REVERT: C 223 LEU cc_start: 0.9109 (mp) cc_final: 0.8900 (mp) REVERT: C 377 TYR cc_start: 0.7950 (m-80) cc_final: 0.7444 (m-80) REVERT: C 559 PHE cc_start: 0.8479 (p90) cc_final: 0.8272 (p90) REVERT: C 647 LEU cc_start: 0.9120 (tp) cc_final: 0.8546 (pp) REVERT: C 728 MET cc_start: 0.9473 (ptm) cc_final: 0.9256 (ptm) REVERT: C 781 GLN cc_start: 0.8831 (mt0) cc_final: 0.8363 (mt0) REVERT: C 916 ASN cc_start: 0.9658 (m-40) cc_final: 0.9452 (m-40) REVERT: C 918 LYS cc_start: 0.9616 (mttt) cc_final: 0.9119 (tptp) REVERT: C 957 ASN cc_start: 0.9484 (m110) cc_final: 0.9023 (m110) REVERT: C 961 LYS cc_start: 0.9351 (mttt) cc_final: 0.8872 (mttt) REVERT: C 999 GLN cc_start: 0.9298 (mp10) cc_final: 0.9006 (mp10) REVERT: C 1011 ARG cc_start: 0.9470 (tpp-160) cc_final: 0.9141 (tpp-160) REVERT: C 1051 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8330 (mm110) REVERT: H 34 MET cc_start: 0.3094 (mpp) cc_final: 0.2491 (mpp) REVERT: H 83 MET cc_start: -0.5830 (ptt) cc_final: -0.6486 (ptt) REVERT: E 73 ASP cc_start: 0.5077 (m-30) cc_final: 0.4498 (p0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.3890 time to fit residues: 244.8252 Evaluate side-chains 311 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 0.9990 chunk 322 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 303 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 655 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.111485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067733 restraints weight = 128327.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069781 restraints weight = 75880.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071092 restraints weight = 49395.585| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31689 Z= 0.184 Angle : 0.595 12.436 43124 Z= 0.315 Chirality : 0.045 0.216 4983 Planarity : 0.004 0.046 5509 Dihedral : 5.499 55.893 5297 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3827 helix: -0.27 (0.19), residues: 681 sheet: -0.13 (0.16), residues: 1005 loop : -0.74 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 433 HIS 0.008 0.001 HIS C1061 PHE 0.033 0.002 PHE C 272 TYR 0.029 0.001 TYR B 204 ARG 0.006 0.001 ARG C 992 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6586.93 seconds wall clock time: 120 minutes 49.39 seconds (7249.39 seconds total)