Starting phenix.real_space_refine on Wed Feb 21 13:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrc_14910/02_2024/7zrc_14910.pdb" } resolution = 3.5 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= 0.027 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 140 5.16 5 C 19524 2.51 5 N 5064 2.21 5 O 5996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30724 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8272 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 54, 'TRANS': 1004} Chain breaks: 7 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: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8249 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 53, 'TRANS': 1002} Chain breaks: 6 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" 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 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 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 Time building chain proxies: 16.42, per 1000 atoms: 0.53 Number of scatterers: 30724 At special positions: 0 Unit cell: (161.85, 161.02, 213.31, 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 140 16.00 O 5996 8.00 N 5064 7.00 C 19524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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=2.02 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=2.03 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " 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 340 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B1071 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 340 " " NAG B1309 " - " ASN B 61 " " 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 B 798 " " NAG E 1 " - " ASN B 714 " " NAG I 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 714 " " NAG O 1 " - " ASN C 798 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C1131 " " NAG R 1 " - " ASN A 714 " " NAG S 1 " - " ASN A 798 " " NAG T 1 " - " ASN A1095 " " NAG U 1 " - " ASN A1131 " Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 6.0 seconds 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 71 sheets defined 21.5% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.640A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.233A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.324A 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 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 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: 3.644A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.139A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.421A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.509A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 4.164A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.331A 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 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 756 through 780 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: 3.845A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.007A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.555A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.536A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.017A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.674A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.210A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.476A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.798A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) 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 883 through 888 removed outlier: 3.743A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.260A 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 removed outlier: 3.549A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) 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 1029 removed outlier: 4.895A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.956A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.120A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.671A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.126A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.676A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.102A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.667A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.890A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.544A pdb=" N ALA B 261 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.669A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.734A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.568A pdb=" N TRP B 433 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.733A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.525A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.264A pdb=" N VAL B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS C 787 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.413A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.645A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.452A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.136A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 6.371A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.630A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.758A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE C 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.602A pdb=" N TRP C 433 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.809A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD3, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.338A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 699 through 701 removed outlier: 3.628A pdb=" N LYS A 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 708 through 712 removed outlier: 4.442A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.015A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 715 through 725 Processing sheet with id=AD8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.524A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.341A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.521A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.922A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.671A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 151 through 162 removed outlier: 5.626A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.636A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.541A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.694A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.485A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.575A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.058A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.459A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.534A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.591A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 107 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY F 100 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE F 105 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.523A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.579A pdb=" N TYR G 49 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR J 33 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY J 100 " --> pdb=" O PHE J 105 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE J 105 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.521A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AH8, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.584A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3558 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: 15.16 Time building geometry restraints manager: 14.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9201 1.33 - 1.45: 5905 1.45 - 1.58: 16127 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 31417 Sorted by residual: bond pdb=" N ILE C 329 " pdb=" CA ILE C 329 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.82e+00 bond pdb=" N TYR C 263 " pdb=" CA TYR C 263 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.16e+00 bond pdb=" N GLN B1033 " pdb=" CA GLN B1033 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.15e+00 bond pdb=" N VAL A 607 " pdb=" CA VAL A 607 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 7.91e+00 bond pdb=" N VAL C 264 " pdb=" CA VAL C 264 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.87e+00 ... (remaining 31412 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 678 105.56 - 112.71: 16799 112.71 - 119.85: 9859 119.85 - 127.00: 15098 127.00 - 134.15: 297 Bond angle restraints: 42731 Sorted by residual: angle pdb=" N GLY C 854 " pdb=" CA GLY C 854 " pdb=" C GLY C 854 " ideal model delta sigma weight residual 114.92 108.42 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" C ASN K 30 " pdb=" CA ASN K 30 " pdb=" CB ASN K 30 " ideal model delta sigma weight residual 117.23 110.84 6.39 1.36e+00 5.41e-01 2.21e+01 angle pdb=" C ALA A 710 " pdb=" N ILE A 711 " pdb=" CA ILE A 711 " ideal model delta sigma weight residual 123.33 119.51 3.82 8.70e-01 1.32e+00 1.92e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 113.30 107.76 5.54 1.34e+00 5.57e-01 1.71e+01 angle pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " pdb=" CG ASN A 61 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 42726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 18373 17.39 - 34.79: 805 34.79 - 52.18: 151 52.18 - 69.58: 30 69.58 - 86.97: 9 Dihedral angle restraints: 19368 sinusoidal: 8188 harmonic: 11180 Sorted by residual: 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 -133.06 47.06 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual -86.00 -132.11 46.11 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4900 0.122 - 0.244: 66 0.244 - 0.366: 2 0.366 - 0.488: 1 0.488 - 0.610: 1 Chirality restraints: 4970 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4967 not shown) Planarity restraints: 5491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.229 2.00e-02 2.50e+03 1.92e-01 4.59e+02 pdb=" C7 NAG A1309 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.317 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.223 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C7 NAG B1302 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.299 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.146 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" C7 NAG A1303 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.022 2.00e-02 2.50e+03 ... (remaining 5488 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 613 2.68 - 3.23: 28624 3.23 - 3.79: 47491 3.79 - 4.34: 66009 4.34 - 4.90: 110829 Nonbonded interactions: 253566 Sorted by model distance: nonbonded pdb=" O ALA A 876 " pdb=" OG1 THR A 880 " model vdw 2.125 2.440 nonbonded pdb=" O ALA C 876 " pdb=" OG1 THR C 880 " model vdw 2.138 2.440 nonbonded pdb=" OE2 GLU B 915 " pdb=" OG SER A1120 " model vdw 2.161 2.440 nonbonded pdb=" O GLY B 877 " pdb=" OG SER B 881 " model vdw 2.163 2.440 nonbonded pdb=" NH1 ARG A 902 " pdb=" O LEU A1046 " model vdw 2.167 2.520 ... (remaining 253561 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 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) selection = (chain 'B' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) selection = (chain 'C' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' 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 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' 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: 3.460 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: 16.610 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 86.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.006 0.062 31417 Z= 0.423 Angle : 0.637 7.676 42731 Z= 0.363 Chirality : 0.049 0.610 4970 Planarity : 0.006 0.192 5451 Dihedral : 10.102 86.971 12048 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 0.99 % Allowed : 4.91 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.03 (0.14), residues: 3797 helix: 1.31 (0.20), residues: 679 sheet: 0.02 (0.16), residues: 1074 loop : -0.44 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1099 HIS 0.006 0.001 HIS C1085 PHE 0.020 0.002 PHE A1118 TYR 0.020 0.001 TYR B1064 ARG 0.005 0.000 ARG C1011 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 398 time to evaluate : 3.272 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: B 54 LEU cc_start: 0.9181 (mt) cc_final: 0.8922 (mp) REVERT: B 177 MET cc_start: -0.2768 (ttm) cc_final: -0.4959 (mmt) REVERT: B 581 ILE cc_start: 0.8881 (mm) cc_final: 0.8659 (mp) REVERT: B 737 MET cc_start: 0.8286 (ttt) cc_final: 0.8037 (ttm) REVERT: B 981 LEU cc_start: 0.8926 (mt) cc_final: 0.8616 (mp) REVERT: C 302 SER cc_start: 0.8878 (t) cc_final: 0.8358 (p) REVERT: C 538 PHE cc_start: 0.8280 (p90) cc_final: 0.8022 (p90) REVERT: C 752 GLN cc_start: 0.8491 (mt0) cc_final: 0.8144 (mm-40) REVERT: C 864 ASP cc_start: 0.8365 (m-30) cc_final: 0.8158 (m-30) REVERT: C 1070 LYS cc_start: 0.8062 (mttt) cc_final: 0.7720 (mtpp) REVERT: A 164 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 773 LYS cc_start: 0.8032 (tttt) cc_final: 0.7813 (ttmm) REVERT: A 856 THR cc_start: 0.8834 (p) cc_final: 0.8629 (t) REVERT: A 954 GLN cc_start: 0.7537 (mm110) cc_final: 0.7252 (tp-100) REVERT: A 957 ASN cc_start: 0.8298 (m-40) cc_final: 0.8056 (m-40) REVERT: A 1007 GLN cc_start: 0.7839 (mt0) cc_final: 0.7621 (mp10) REVERT: H 48 MET cc_start: 0.1604 (mtp) cc_final: 0.1037 (ptm) outliers start: 33 outliers final: 15 residues processed: 428 average time/residue: 0.4385 time to fit residues: 300.7997 Evaluate side-chains 267 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.5980 chunk 286 optimal weight: 0.7980 chunk 158 optimal weight: 0.0030 chunk 97 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 40.0000 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN B 164 ASN B 196 ASN B 752 GLN B 904 ASN B 952 ASN B 954 GLN B 962 GLN B1007 GLN B1116 ASN C 318 GLN C 561 GLN C 759 GLN C 946 GLN C 952 ASN C 962 GLN C1007 GLN A 560 GLN A 577 GLN A 610 GLN A 672 GLN A 910 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 966 ASN L 101 GLN G 101 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31417 Z= 0.186 Angle : 0.507 9.892 42731 Z= 0.265 Chirality : 0.043 0.353 4970 Planarity : 0.004 0.048 5451 Dihedral : 6.278 58.145 5258 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 7.75 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3797 helix: 1.78 (0.20), residues: 673 sheet: 0.14 (0.16), residues: 1102 loop : -0.35 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.004 0.001 HIS A 49 PHE 0.016 0.001 PHE A 32 TYR 0.019 0.001 TYR B 262 ARG 0.003 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 262 time to evaluate : 3.184 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: B 177 MET cc_start: -0.2745 (ttm) cc_final: -0.4829 (mmt) REVERT: B 581 ILE cc_start: 0.8924 (mm) cc_final: 0.8691 (mp) REVERT: B 658 GLU cc_start: 0.7889 (pm20) cc_final: 0.7561 (pm20) REVERT: B 737 MET cc_start: 0.8248 (ttt) cc_final: 0.7940 (ttm) REVERT: B 954 GLN cc_start: 0.7999 (tt0) cc_final: 0.7638 (tp40) REVERT: B 981 LEU cc_start: 0.8922 (mt) cc_final: 0.8632 (mp) REVERT: C 177 MET cc_start: -0.3062 (mtp) cc_final: -0.3870 (mmt) REVERT: C 302 SER cc_start: 0.8773 (t) cc_final: 0.8353 (p) REVERT: C 733 VAL cc_start: 0.8041 (t) cc_final: 0.7792 (p) REVERT: C 736 THR cc_start: 0.9069 (m) cc_final: 0.8683 (p) REVERT: C 752 GLN cc_start: 0.8390 (mt0) cc_final: 0.8076 (mm-40) REVERT: C 864 ASP cc_start: 0.8414 (m-30) cc_final: 0.8186 (m-30) REVERT: C 1042 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7307 (mtpp) REVERT: A 749 LEU cc_start: 0.8973 (mt) cc_final: 0.8749 (mp) REVERT: A 773 LYS cc_start: 0.7974 (tttt) cc_final: 0.7584 (ttpp) REVERT: A 856 THR cc_start: 0.8779 (p) cc_final: 0.8558 (t) REVERT: H 48 MET cc_start: 0.1503 (mtp) cc_final: 0.0932 (ptm) REVERT: F 31 MET cc_start: 0.5243 (pmm) cc_final: 0.4880 (mmp) outliers start: 49 outliers final: 31 residues processed: 300 average time/residue: 0.3976 time to fit residues: 198.9256 Evaluate side-chains 250 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 371 optimal weight: 30.0000 chunk 306 optimal weight: 0.7980 chunk 341 optimal weight: 0.8980 chunk 117 optimal weight: 30.0000 chunk 275 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN B1051 GLN B1105 ASN C 537 ASN C 932 GLN C 957 ASN C1085 HIS A 49 HIS ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31417 Z= 0.266 Angle : 0.520 8.783 42731 Z= 0.271 Chirality : 0.045 0.317 4970 Planarity : 0.004 0.066 5451 Dihedral : 5.689 58.339 5250 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.24 % Allowed : 8.80 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.17 (0.14), residues: 3797 helix: 1.66 (0.20), residues: 674 sheet: 0.12 (0.15), residues: 1107 loop : -0.36 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.005 0.001 HIS B 207 PHE 0.019 0.001 PHE A 339 TYR 0.019 0.001 TYR B 262 ARG 0.006 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 226 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2680 (ttm) cc_final: -0.4812 (mmt) REVERT: B 658 GLU cc_start: 0.7937 (pm20) cc_final: 0.7642 (pm20) REVERT: B 737 MET cc_start: 0.8339 (ttt) cc_final: 0.7994 (ttm) REVERT: B 947 ASP cc_start: 0.8105 (m-30) cc_final: 0.7836 (m-30) REVERT: B 981 LEU cc_start: 0.8981 (mt) cc_final: 0.8681 (mp) REVERT: C 302 SER cc_start: 0.8912 (t) cc_final: 0.8484 (p) REVERT: C 733 VAL cc_start: 0.8015 (t) cc_final: 0.7752 (p) REVERT: C 752 GLN cc_start: 0.8411 (mt0) cc_final: 0.8123 (mm-40) REVERT: C 1042 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7337 (mtpp) REVERT: A 299 THR cc_start: 0.8864 (m) cc_final: 0.8537 (p) REVERT: A 303 PHE cc_start: 0.9149 (m-80) cc_final: 0.8943 (m-80) REVERT: A 749 LEU cc_start: 0.9029 (mt) cc_final: 0.8810 (mp) REVERT: A 773 LYS cc_start: 0.8005 (tttt) cc_final: 0.7663 (ttpp) REVERT: A 856 THR cc_start: 0.8721 (p) cc_final: 0.8503 (t) REVERT: H 48 MET cc_start: 0.1356 (mtp) cc_final: 0.0830 (ptm) REVERT: F 31 MET cc_start: 0.5219 (pmm) cc_final: 0.4931 (mmp) REVERT: F 48 MET cc_start: 0.2306 (OUTLIER) cc_final: 0.2065 (pmm) outliers start: 75 outliers final: 53 residues processed: 288 average time/residue: 0.3933 time to fit residues: 190.4967 Evaluate side-chains 263 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 40.0000 chunk 258 optimal weight: 0.0870 chunk 178 optimal weight: 0.5980 chunk 38 optimal weight: 50.0000 chunk 164 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 327 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 ASN C 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31417 Z= 0.231 Angle : 0.496 7.371 42731 Z= 0.258 Chirality : 0.044 0.310 4970 Planarity : 0.004 0.065 5451 Dihedral : 5.277 58.425 5250 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.33 % Allowed : 9.66 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.25 (0.14), residues: 3797 helix: 1.73 (0.20), residues: 674 sheet: 0.18 (0.15), residues: 1111 loop : -0.33 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.004 0.001 HIS A 207 PHE 0.016 0.001 PHE C 756 TYR 0.018 0.001 TYR B1064 ARG 0.004 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 3.414 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: B 177 MET cc_start: -0.2660 (ttm) cc_final: -0.4765 (mmt) REVERT: B 658 GLU cc_start: 0.7947 (pm20) cc_final: 0.7647 (pm20) REVERT: B 737 MET cc_start: 0.8321 (ttt) cc_final: 0.7967 (ttm) REVERT: B 742 ASP cc_start: 0.5618 (t0) cc_final: 0.5417 (t0) REVERT: B 947 ASP cc_start: 0.8082 (m-30) cc_final: 0.7837 (m-30) REVERT: B 981 LEU cc_start: 0.8977 (mt) cc_final: 0.8713 (mp) REVERT: C 302 SER cc_start: 0.8917 (t) cc_final: 0.8520 (p) REVERT: C 752 GLN cc_start: 0.8411 (mt0) cc_final: 0.8086 (mm110) REVERT: C 1042 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7350 (mtpp) REVERT: A 299 THR cc_start: 0.8857 (m) cc_final: 0.8506 (p) REVERT: A 749 LEU cc_start: 0.9025 (mt) cc_final: 0.8785 (mp) REVERT: A 773 LYS cc_start: 0.7986 (tttt) cc_final: 0.7647 (ttpp) REVERT: A 856 THR cc_start: 0.8715 (p) cc_final: 0.8498 (t) REVERT: A 1042 LYS cc_start: 0.7678 (tttt) cc_final: 0.7180 (mptt) REVERT: H 48 MET cc_start: 0.1275 (mtp) cc_final: 0.0801 (ptm) REVERT: F 31 MET cc_start: 0.5209 (pmm) cc_final: 0.4957 (mmp) outliers start: 78 outliers final: 58 residues processed: 285 average time/residue: 0.3806 time to fit residues: 185.0498 Evaluate side-chains 268 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 209 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 311 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 186 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 ASN C 946 GLN C 957 ASN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31417 Z= 0.282 Angle : 0.508 7.291 42731 Z= 0.265 Chirality : 0.044 0.306 4970 Planarity : 0.004 0.068 5451 Dihedral : 5.081 57.995 5250 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.63 % Allowed : 9.84 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3797 helix: 1.68 (0.20), residues: 671 sheet: 0.18 (0.15), residues: 1096 loop : -0.33 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.004 0.001 HIS B1045 PHE 0.015 0.001 PHE A1118 TYR 0.019 0.001 TYR B1064 ARG 0.003 0.000 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 221 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5568 (pt) REVERT: B 177 MET cc_start: -0.2726 (ttm) cc_final: -0.4677 (mmt) REVERT: B 737 MET cc_start: 0.8342 (ttt) cc_final: 0.7979 (ttm) REVERT: B 947 ASP cc_start: 0.8136 (m-30) cc_final: 0.7870 (m-30) REVERT: B 981 LEU cc_start: 0.8984 (mt) cc_final: 0.8736 (mp) REVERT: C 302 SER cc_start: 0.8963 (t) cc_final: 0.8579 (p) REVERT: C 752 GLN cc_start: 0.8417 (mt0) cc_final: 0.8102 (mm110) REVERT: C 985 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: C 1042 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7393 (mtpp) REVERT: A 299 THR cc_start: 0.8855 (m) cc_final: 0.8486 (p) REVERT: A 773 LYS cc_start: 0.7989 (tttt) cc_final: 0.7658 (ttpp) REVERT: A 856 THR cc_start: 0.8688 (p) cc_final: 0.8458 (t) REVERT: H 48 MET cc_start: 0.1174 (mtp) cc_final: 0.0737 (ptm) REVERT: F 31 MET cc_start: 0.5247 (pmm) cc_final: 0.5033 (mmp) outliers start: 88 outliers final: 67 residues processed: 292 average time/residue: 0.3789 time to fit residues: 187.6270 Evaluate side-chains 282 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 212 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 10.0000 chunk 329 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 365 optimal weight: 40.0000 chunk 303 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 30 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 ASN A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31417 Z= 0.278 Angle : 0.507 8.088 42731 Z= 0.265 Chirality : 0.045 0.302 4970 Planarity : 0.004 0.066 5451 Dihedral : 4.985 56.485 5250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 10.32 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3797 helix: 1.73 (0.20), residues: 658 sheet: 0.23 (0.15), residues: 1094 loop : -0.37 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.003 0.001 HIS A 49 PHE 0.014 0.001 PHE A1118 TYR 0.018 0.001 TYR B1064 ARG 0.003 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 215 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5513 (pt) REVERT: B 177 MET cc_start: -0.2819 (ttm) cc_final: -0.4524 (mmt) REVERT: B 658 GLU cc_start: 0.7997 (pm20) cc_final: 0.7613 (pm20) REVERT: B 737 MET cc_start: 0.8341 (ttt) cc_final: 0.7974 (ttm) REVERT: B 947 ASP cc_start: 0.8134 (m-30) cc_final: 0.7889 (m-30) REVERT: B 954 GLN cc_start: 0.7994 (tt0) cc_final: 0.7676 (tp40) REVERT: B 981 LEU cc_start: 0.8975 (mt) cc_final: 0.8733 (mp) REVERT: C 32 PHE cc_start: 0.8240 (m-80) cc_final: 0.7922 (m-80) REVERT: C 302 SER cc_start: 0.8970 (t) cc_final: 0.8582 (p) REVERT: C 752 GLN cc_start: 0.8390 (mt0) cc_final: 0.8094 (mm110) REVERT: C 985 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: C 1042 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7445 (mtpp) REVERT: A 299 THR cc_start: 0.8865 (m) cc_final: 0.8491 (p) REVERT: A 773 LYS cc_start: 0.8017 (tttt) cc_final: 0.7678 (ttpp) REVERT: A 856 THR cc_start: 0.8701 (p) cc_final: 0.8484 (t) REVERT: H 48 MET cc_start: 0.1118 (mtp) cc_final: 0.0697 (ptm) REVERT: K 4 MET cc_start: 0.3446 (tmm) cc_final: 0.2932 (tpt) outliers start: 86 outliers final: 76 residues processed: 287 average time/residue: 0.3882 time to fit residues: 189.0740 Evaluate side-chains 288 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 209 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 10.0000 chunk 41 optimal weight: 50.0000 chunk 208 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 307 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 364 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31417 Z= 0.235 Angle : 0.498 8.319 42731 Z= 0.259 Chirality : 0.044 0.296 4970 Planarity : 0.003 0.065 5451 Dihedral : 4.838 54.617 5250 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.42 % Allowed : 10.77 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.29 (0.14), residues: 3797 helix: 1.87 (0.20), residues: 652 sheet: 0.28 (0.15), residues: 1094 loop : -0.36 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.029 0.001 PHE B 487 TYR 0.017 0.001 TYR B1064 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 214 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2904 (ttm) cc_final: -0.4373 (mmt) REVERT: B 658 GLU cc_start: 0.8019 (pm20) cc_final: 0.7617 (pm20) REVERT: B 737 MET cc_start: 0.8325 (ttt) cc_final: 0.7965 (ttm) REVERT: B 947 ASP cc_start: 0.8121 (m-30) cc_final: 0.7875 (m-30) REVERT: B 954 GLN cc_start: 0.7962 (tt0) cc_final: 0.7676 (tp40) REVERT: B 981 LEU cc_start: 0.8978 (mt) cc_final: 0.8758 (mp) REVERT: C 32 PHE cc_start: 0.8232 (m-80) cc_final: 0.7936 (m-80) REVERT: C 177 MET cc_start: -0.3363 (mmt) cc_final: -0.4772 (mtt) REVERT: C 302 SER cc_start: 0.8981 (t) cc_final: 0.8577 (p) REVERT: C 752 GLN cc_start: 0.8365 (mt0) cc_final: 0.8077 (mm110) REVERT: C 985 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: C 1042 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7421 (mtpp) REVERT: A 299 THR cc_start: 0.8867 (m) cc_final: 0.8494 (p) REVERT: A 773 LYS cc_start: 0.8019 (tttt) cc_final: 0.7725 (ttpp) REVERT: A 856 THR cc_start: 0.8702 (p) cc_final: 0.8477 (t) REVERT: H 48 MET cc_start: 0.1119 (mtp) cc_final: 0.0693 (ptm) REVERT: K 4 MET cc_start: 0.3454 (tmm) cc_final: 0.2955 (tpt) outliers start: 81 outliers final: 73 residues processed: 283 average time/residue: 0.3872 time to fit residues: 187.1259 Evaluate side-chains 282 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 207 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 10.0000 chunk 145 optimal weight: 50.0000 chunk 217 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 GLN C 957 ASN A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31417 Z= 0.186 Angle : 0.476 9.109 42731 Z= 0.248 Chirality : 0.043 0.289 4970 Planarity : 0.003 0.067 5451 Dihedral : 4.613 50.601 5250 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 2.21 % Allowed : 11.31 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.39 (0.14), residues: 3797 helix: 1.96 (0.20), residues: 665 sheet: 0.35 (0.15), residues: 1087 loop : -0.31 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.002 0.000 HIS A 207 PHE 0.020 0.001 PHE B 487 TYR 0.020 0.001 TYR K 49 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 212 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2979 (ttm) cc_final: -0.4421 (mmt) REVERT: B 658 GLU cc_start: 0.8004 (pm20) cc_final: 0.7595 (pm20) REVERT: B 737 MET cc_start: 0.8311 (ttt) cc_final: 0.7926 (ttm) REVERT: B 947 ASP cc_start: 0.8100 (m-30) cc_final: 0.7855 (m-30) REVERT: B 954 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7607 (tp40) REVERT: B 981 LEU cc_start: 0.8951 (mt) cc_final: 0.8741 (mp) REVERT: C 32 PHE cc_start: 0.8205 (m-80) cc_final: 0.8000 (m-80) REVERT: C 302 SER cc_start: 0.8999 (t) cc_final: 0.8607 (p) REVERT: C 752 GLN cc_start: 0.8335 (mt0) cc_final: 0.8037 (mm110) REVERT: C 1042 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7450 (mtpp) REVERT: A 773 LYS cc_start: 0.7980 (tttt) cc_final: 0.7639 (ttpp) REVERT: A 856 THR cc_start: 0.8693 (p) cc_final: 0.8455 (t) REVERT: A 1007 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: H 48 MET cc_start: 0.1124 (mtp) cc_final: 0.0634 (ptm) REVERT: K 4 MET cc_start: 0.3207 (tmm) cc_final: 0.2759 (tpt) outliers start: 74 outliers final: 62 residues processed: 277 average time/residue: 0.3718 time to fit residues: 175.4834 Evaluate side-chains 266 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.2980 chunk 349 optimal weight: 30.0000 chunk 318 optimal weight: 40.0000 chunk 339 optimal weight: 50.0000 chunk 348 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 266 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31417 Z= 0.304 Angle : 0.518 8.999 42731 Z= 0.269 Chirality : 0.045 0.297 4970 Planarity : 0.004 0.071 5451 Dihedral : 4.740 43.908 5249 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 11.22 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.28 (0.14), residues: 3797 helix: 1.73 (0.20), residues: 666 sheet: 0.32 (0.15), residues: 1093 loop : -0.35 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.003 0.001 HIS B1045 PHE 0.017 0.001 PHE B1118 TYR 0.021 0.001 TYR K 49 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 199 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2904 (ttm) cc_final: -0.4373 (mmt) REVERT: B 200 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.5876 (t80) REVERT: B 228 ASP cc_start: 0.7548 (p0) cc_final: 0.7187 (p0) REVERT: B 658 GLU cc_start: 0.8019 (pm20) cc_final: 0.7697 (pm20) REVERT: B 737 MET cc_start: 0.8356 (ttt) cc_final: 0.7981 (ttm) REVERT: B 947 ASP cc_start: 0.8141 (m-30) cc_final: 0.7889 (m-30) REVERT: B 954 GLN cc_start: 0.7906 (tt0) cc_final: 0.7663 (tp40) REVERT: B 981 LEU cc_start: 0.8967 (mt) cc_final: 0.8737 (mp) REVERT: C 32 PHE cc_start: 0.8267 (m-80) cc_final: 0.8041 (m-80) REVERT: C 177 MET cc_start: -0.3217 (mmt) cc_final: -0.4488 (mtt) REVERT: C 233 ILE cc_start: 0.4794 (OUTLIER) cc_final: 0.4587 (pt) REVERT: C 302 SER cc_start: 0.8989 (t) cc_final: 0.8591 (p) REVERT: C 752 GLN cc_start: 0.8351 (mt0) cc_final: 0.8071 (mm110) REVERT: C 985 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: C 1042 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7442 (mtpp) REVERT: A 773 LYS cc_start: 0.8018 (tttt) cc_final: 0.7661 (ttpp) REVERT: A 856 THR cc_start: 0.8724 (p) cc_final: 0.8486 (t) REVERT: A 1007 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: H 48 MET cc_start: 0.1243 (mtp) cc_final: 0.0694 (ptm) REVERT: K 4 MET cc_start: 0.3166 (tmm) cc_final: 0.2769 (tpt) outliers start: 79 outliers final: 70 residues processed: 267 average time/residue: 0.4094 time to fit residues: 186.8752 Evaluate side-chains 268 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 193 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 50.0000 chunk 222 optimal weight: 0.9990 chunk 359 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 chunk 249 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 346 optimal weight: 50.0000 chunk 299 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS ** C 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 31417 Z= 0.486 Angle : 0.603 10.953 42731 Z= 0.313 Chirality : 0.048 0.315 4970 Planarity : 0.004 0.072 5451 Dihedral : 5.189 48.515 5249 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.36 % Allowed : 11.37 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3797 helix: 1.16 (0.20), residues: 667 sheet: 0.18 (0.15), residues: 1103 loop : -0.47 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 104 HIS 0.007 0.001 HIS A1045 PHE 0.023 0.002 PHE B1118 TYR 0.030 0.001 TYR C1135 ARG 0.006 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 198 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2630 (ttm) cc_final: -0.4166 (mmt) REVERT: B 200 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.6237 (t80) REVERT: B 947 ASP cc_start: 0.8158 (m-30) cc_final: 0.7839 (m-30) REVERT: B 954 GLN cc_start: 0.8060 (tt0) cc_final: 0.7708 (tp40) REVERT: C 233 ILE cc_start: 0.4944 (OUTLIER) cc_final: 0.4695 (pt) REVERT: C 302 SER cc_start: 0.8968 (t) cc_final: 0.8571 (p) REVERT: C 752 GLN cc_start: 0.8391 (mt0) cc_final: 0.8190 (mm-40) REVERT: C 985 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: C 1042 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (mtpp) REVERT: A 749 LEU cc_start: 0.9136 (mt) cc_final: 0.8813 (mp) REVERT: A 856 THR cc_start: 0.8758 (p) cc_final: 0.8509 (t) REVERT: H 48 MET cc_start: 0.1293 (mtp) cc_final: 0.0703 (ptm) outliers start: 79 outliers final: 70 residues processed: 266 average time/residue: 0.3729 time to fit residues: 170.7058 Evaluate side-chains 269 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 195 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.5980 chunk 238 optimal weight: 0.8980 chunk 319 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 276 optimal weight: 0.6980 chunk 44 optimal weight: 30.0000 chunk 83 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 308 optimal weight: 0.5980 chunk 38 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.206148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.200668 restraints weight = 39365.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.179706 restraints weight = 103854.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.169524 restraints weight = 114236.380| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31417 Z= 0.177 Angle : 0.498 10.430 42731 Z= 0.257 Chirality : 0.043 0.284 4970 Planarity : 0.003 0.066 5451 Dihedral : 4.666 43.508 5249 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.65 % Allowed : 12.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.31 (0.14), residues: 3797 helix: 1.84 (0.20), residues: 662 sheet: 0.31 (0.16), residues: 1092 loop : -0.35 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.002 0.001 HIS B1085 PHE 0.015 0.001 PHE A 344 TYR 0.020 0.001 TYR C1135 ARG 0.005 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6059.17 seconds wall clock time: 112 minutes 15.37 seconds (6735.37 seconds total)