Starting phenix.real_space_refine on Mon Apr 6 07:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtt_21383/04_2026/6vtt_21383.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 sd= 0.071 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 110 5.16 5 C 10385 2.51 5 N 2712 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16607 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3400 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Chain: "E" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 5 Chain: "G" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3448 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "H" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1026 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1012 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" 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: "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: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" 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: 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: "C" 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 Time building chain proxies: 3.57, per 1000 atoms: 0.21 Number of scatterers: 16607 At special positions: 0 Unit cell: (128.244, 128.244, 167.703, 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 110 16.00 O 3400 8.00 N 2712 7.00 C 10385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1611 " - " ASN C 611 " " NAG C1637 " - " ASN C 637 " " NAG D 1 " - " ASN F 130 " " NAG E1088 " - " ASN E 88 " " NAG E1130 " - " ASN E 130 " " NAG E1156 " - " ASN E 156 " " NAG E1160 " - " ASN E 160 " " NAG E1230 " - " ASN E 230 " " NAG E1241 " - " ASN E 241 " " NAG E1276 " - " ASN E 276 " " NAG E1289 " - " ASN E 289 " " NAG E1301 " - " ASN E 301 " " NAG E1332 " - " ASN E 332 " " NAG E1356 " - " ASN E 356 " " NAG E1362 " - " ASN E 362 " " NAG E1442 " - " ASN E 442 " " NAG E1443 " - " ASN E 448 " " NAG E1502 " - " ASN E 502 " " NAG F1088 " - " ASN F 88 " " NAG F1234 " - " ASN F 234 " " NAG F1289 " - " ASN F 289 " " NAG F1301 " - " ASN F 301 " " NAG F1356 " - " ASN F 356 " " NAG F1362 " - " ASN F 362 " " NAG F1386 " - " ASN F 386 " " NAG F1442 " - " ASN F 442 " " NAG F1448 " - " ASN F 448 " " NAG F1502 " - " ASN F 502 " " NAG G1088 " - " ASN G 88 " " NAG G1234 " - " ASN G 234 " " NAG G1276 " - " ASN G 276 " " NAG G1301 " - " ASN G 301 " " NAG G1356 " - " ASN G 356 " " NAG G1362 " - " ASN G 362 " " NAG G1386 " - " ASN G 386 " " NAG G1442 " - " ASN G 442 " " NAG G1448 " - " ASN G 448 " " NAG G1502 " - " ASN G 502 " " NAG I 1 " - " ASN F 156 " " NAG J 1 " - " ASN F 160 " " NAG K 1 " - " ASN F 197 " " NAG M 1 " - " ASN F 230 " " NAG N 1 " - " ASN F 241 " " NAG O 1 " - " ASN F 262 " " NAG P 1 " - " ASN F 276 " " NAG Q 1 " - " ASN F 332 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 234 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN G 130 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 230 " " NAG a 1 " - " ASN G 241 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 289 " " NAG d 1 " - " ASN G 332 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 585.3 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 38 sheets defined 21.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.569A pdb=" N HIS F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 349 removed outlier: 3.649A pdb=" N THR F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 353 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.565A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.959A pdb=" N SER E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.718A pdb=" N LYS E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 removed outlier: 3.575A pdb=" N SER E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.781A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.603A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.686A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 356 removed outlier: 3.910A pdb=" N ARG G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 349 " --> pdb=" O VAL G 345 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG G 350 " --> pdb=" O SER G 346 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.858A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.737A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.944A pdb=" N TRP H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.962A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.582A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.936A pdb=" N PHE A 519 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 521 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 522 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 removed outlier: 3.507A pdb=" N ALA A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 529 through 542 removed outlier: 4.306A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.710A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.925A pdb=" N ILE A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 623 " --> pdb=" O TYR A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 623' Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.530A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.855A pdb=" N LYS A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 4.338A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 539 " --> pdb=" O ASN B 535 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.735A pdb=" N GLU B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.067A pdb=" N ILE B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP B 623 " --> pdb=" O TYR B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.548A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 640 through 658 removed outlier: 3.654A pdb=" N LYS B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 520 removed outlier: 3.689A pdb=" N PHE C 519 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 520 " --> pdb=" O GLY C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 520' Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.935A pdb=" N LEU C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL C 539 " --> pdb=" O ASN C 535 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 595 removed outlier: 3.558A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.577A pdb=" N TRP C 623 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 633 removed outlier: 3.606A pdb=" N ARG C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 659 removed outlier: 3.620A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 92 through 93 removed outlier: 3.926A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 181 through 185 removed outlier: 7.452A pdb=" N GLU F 190 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.864A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.942A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N LYS F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL F 292 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.942A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N LYS F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL F 292 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS F 385 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.507A pdb=" N PHE F 317 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 358 through 361 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.074A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.655A pdb=" N THR E 244 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.387A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.016A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'E' and resid 181 through 185 removed outlier: 7.842A pdb=" N GLU E 190 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 271 through 273 Processing sheet with id=AC1, first strand: chain 'E' and resid 292 through 297 removed outlier: 3.975A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.900A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS E 305 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR E 318 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 330 through 331 Processing sheet with id=AC4, first strand: chain 'E' and resid 376 through 378 Processing sheet with id=AC5, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC6, first strand: chain 'G' and resid 494 through 499 removed outlier: 4.944A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC9, first strand: chain 'G' and resid 132 through 133 removed outlier: 4.725A pdb=" N ARG G 171 " --> pdb=" O GLU H 100B" (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLU H 100B" --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 14.969A pdb=" N TYR G 173 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 19.152A pdb=" N GLU H 100 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS H 100A" --> pdb=" O SER H 100T" (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER H 100T" --> pdb=" O CYS H 100A" (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU H 100C" --> pdb=" O ALA H 100R" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'G' and resid 201 through 203 Processing sheet with id=AD3, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.630A pdb=" N ILE G 271 " --> pdb=" O HIS G 287 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 377 through 378 removed outlier: 3.641A pdb=" N CYS G 378 " --> pdb=" O GLU G 381 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS G 296 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.421A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY H 10 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY H 10 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 94 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.410A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.966A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.966A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1152 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: 2.40 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5123 1.34 - 1.47: 4326 1.47 - 1.60: 7326 1.60 - 1.73: 2 1.73 - 1.86: 144 Bond restraints: 16921 Sorted by residual: bond pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.543 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.548 0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" N GLU H 100C" pdb=" CA GLU H 100C" ideal model delta sigma weight residual 1.460 1.486 -0.026 1.17e-02 7.31e+03 5.03e+00 ... (remaining 16916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.74: 22922 5.74 - 11.48: 27 11.48 - 17.21: 3 17.21 - 22.95: 3 22.95 - 28.69: 4 Bond angle restraints: 22959 Sorted by residual: angle pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 115.38 86.69 28.69 3.00e+00 1.11e-01 9.14e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 115.16 86.70 28.46 3.00e+00 1.11e-01 9.00e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O2 TYS H 100I" ideal model delta sigma weight residual 114.11 85.86 28.25 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" pdb=" O2 TYS H 100H" ideal model delta sigma weight residual 114.11 86.76 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" OH TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 100.21 119.65 -19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 22954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 10786 22.40 - 44.80: 495 44.80 - 67.20: 108 67.20 - 89.60: 46 89.60 - 112.00: 28 Dihedral angle restraints: 11463 sinusoidal: 5922 harmonic: 5541 Sorted by residual: dihedral pdb=" C ARG F 192 " pdb=" N ARG F 192 " pdb=" CA ARG F 192 " pdb=" CB ARG F 192 " ideal model delta harmonic sigma weight residual -122.60 -105.76 -16.84 0 2.50e+00 1.60e-01 4.54e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -133.75 47.75 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 11460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2678 0.095 - 0.189: 179 0.189 - 0.284: 17 0.284 - 0.378: 3 0.378 - 0.473: 3 Chirality restraints: 2880 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.24e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.88e+01 ... (remaining 2877 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " -0.367 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG V 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " 0.558 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1088 " -0.120 2.00e-02 2.50e+03 9.65e-02 1.16e+02 pdb=" C7 NAG G1088 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G1088 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG G1088 " 0.149 2.00e-02 2.50e+03 pdb=" O7 NAG G1088 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 87 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLU G 87 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU G 87 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN G 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1922 2.75 - 3.29: 15557 3.29 - 3.83: 24992 3.83 - 4.36: 28809 4.36 - 4.90: 50112 Nonbonded interactions: 121392 Sorted by model distance: nonbonded pdb=" O4 MAN V 6 " pdb=" O6 MAN V 6 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS A 604 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN F 258 " pdb=" OG1 THR F 387 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN E 363 " pdb=" OG SER E 388 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU E 164 " pdb=" CB ASN G 197 " model vdw 2.271 3.440 ... (remaining 121387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 513 through 566 or resid 568 through 660 or resid 1611 thr \ ough 1637)) selection = (chain 'C' and (resid 513 through 544 or resid 568 through 660 or resid 1611 thr \ ough 1637)) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 34 through 60 or resid 65 through 135 or resid 152 through \ 186 or resid 189 through 394 or resid 411 through 504 or resid 1130 through 133 \ 2)) selection = (chain 'F' and (resid 34 through 60 or resid 65 through 186 or resid 189 through \ 459 or resid 464 through 504 or resid 1234 through 1502)) selection = (chain 'G' and (resid 34 through 135 or resid 152 through 394 or resid 411 throu \ gh 459 or resid 464 through 504 or resid 1088 through 1448)) } ncs_group { reference = chain 'K' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'V' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.005 0.174 17057 Z= 0.252 Angle : 0.848 28.688 23334 Z= 0.357 Chirality : 0.052 0.473 2880 Planarity : 0.007 0.315 2776 Dihedral : 14.724 112.005 7782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.15), residues: 1872 helix: -4.20 (0.13), residues: 330 sheet: -2.46 (0.21), residues: 433 loop : -3.05 (0.15), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 192 TYR 0.004 0.001 TYR G 484 PHE 0.008 0.001 PHE F 233 TRP 0.007 0.001 TRP F 338 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00501 (16921) covalent geometry : angle 0.82473 (22959) SS BOND : bond 0.00353 ( 33) SS BOND : angle 1.06484 ( 66) hydrogen bonds : bond 0.29816 ( 409) hydrogen bonds : angle 10.50917 ( 1152) link_ALPHA1-2 : bond 0.00353 ( 1) link_ALPHA1-2 : angle 1.61533 ( 3) link_ALPHA1-3 : bond 0.00298 ( 6) link_ALPHA1-3 : angle 2.28241 ( 18) link_ALPHA1-6 : bond 0.00374 ( 4) link_ALPHA1-6 : angle 1.54656 ( 12) link_BETA1-4 : bond 0.00489 ( 29) link_BETA1-4 : angle 1.84522 ( 87) link_NAG-ASN : bond 0.00408 ( 63) link_NAG-ASN : angle 1.89024 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.7974 (p0) cc_final: 0.7635 (p0) REVERT: F 217 TYR cc_start: 0.7698 (m-10) cc_final: 0.7463 (m-10) REVERT: E 107 ASP cc_start: 0.7943 (t0) cc_final: 0.7533 (t0) REVERT: E 258 GLN cc_start: 0.8273 (mt0) cc_final: 0.8054 (mt0) REVERT: H 28 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7662 (ptp90) REVERT: H 30 ASP cc_start: 0.8593 (p0) cc_final: 0.8103 (p0) REVERT: H 32 TYR cc_start: 0.6783 (m-80) cc_final: 0.6176 (m-10) REVERT: H 34 MET cc_start: 0.8396 (mmm) cc_final: 0.7953 (mpp) REVERT: H 38 ARG cc_start: 0.6893 (ptt180) cc_final: 0.5756 (ptp-170) REVERT: H 39 GLN cc_start: 0.7360 (tt0) cc_final: 0.6746 (tt0) REVERT: H 48 VAL cc_start: 0.5732 (t) cc_final: 0.5486 (t) REVERT: H 51 ILE cc_start: 0.9072 (tt) cc_final: 0.8407 (mm) REVERT: H 64 TRP cc_start: 0.6877 (m-10) cc_final: 0.6364 (m-90) REVERT: H 101 ILE cc_start: 0.8644 (mm) cc_final: 0.8404 (pt) REVERT: L 50 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7970 (tm-30) REVERT: L 87 TYR cc_start: 0.5341 (m-80) cc_final: 0.4553 (m-80) REVERT: B 584 GLU cc_start: 0.8215 (tp30) cc_final: 0.7999 (mm-30) REVERT: B 595 MET cc_start: 0.7380 (mtm) cc_final: 0.7063 (mtm) REVERT: C 607 ASN cc_start: 0.8543 (t0) cc_final: 0.8247 (t0) REVERT: C 620 ASN cc_start: 0.8115 (t0) cc_final: 0.7747 (t0) REVERT: C 657 GLU cc_start: 0.9039 (tp30) cc_final: 0.8812 (tt0) REVERT: C 658 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8154 (mptt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1657 time to fit residues: 46.2486 Evaluate side-chains 128 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN E 216 HIS G 66 HIS ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 280 ASN G 330 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076391 restraints weight = 41762.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080027 restraints weight = 24771.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080589 restraints weight = 15579.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081241 restraints weight = 13428.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081824 restraints weight = 11550.510| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17057 Z= 0.166 Angle : 0.663 11.912 23334 Z= 0.311 Chirality : 0.047 0.258 2880 Planarity : 0.004 0.034 2776 Dihedral : 12.872 92.560 4176 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.83 % Allowed : 8.32 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.17), residues: 1872 helix: -2.16 (0.23), residues: 334 sheet: -2.01 (0.22), residues: 475 loop : -2.62 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 170 TYR 0.022 0.001 TYR L 36 PHE 0.014 0.002 PHE G 93 TRP 0.024 0.001 TRP F 35 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00376 (16921) covalent geometry : angle 0.62594 (22959) SS BOND : bond 0.00332 ( 33) SS BOND : angle 0.86858 ( 66) hydrogen bonds : bond 0.05958 ( 409) hydrogen bonds : angle 6.60910 ( 1152) link_ALPHA1-2 : bond 0.00565 ( 1) link_ALPHA1-2 : angle 2.11651 ( 3) link_ALPHA1-3 : bond 0.01062 ( 6) link_ALPHA1-3 : angle 2.15845 ( 18) link_ALPHA1-6 : bond 0.00549 ( 4) link_ALPHA1-6 : angle 1.91306 ( 12) link_BETA1-4 : bond 0.00551 ( 29) link_BETA1-4 : angle 1.79910 ( 87) link_NAG-ASN : bond 0.00356 ( 63) link_NAG-ASN : angle 2.03682 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8048 (p0) cc_final: 0.7786 (p0) REVERT: E 192 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7147 (ttm170) REVERT: G 302 MET cc_start: 0.8558 (mmt) cc_final: 0.8274 (mmp) REVERT: H 30 ASP cc_start: 0.8254 (p0) cc_final: 0.7868 (p0) REVERT: H 38 ARG cc_start: 0.7386 (ptt180) cc_final: 0.6808 (ptp90) REVERT: H 51 ILE cc_start: 0.9127 (tt) cc_final: 0.8557 (mm) REVERT: H 64 TRP cc_start: 0.6630 (m-10) cc_final: 0.6327 (m-90) REVERT: L 32 PHE cc_start: 0.7286 (m-80) cc_final: 0.6972 (m-80) REVERT: L 87 TYR cc_start: 0.6220 (m-80) cc_final: 0.5990 (m-80) REVERT: C 607 ASN cc_start: 0.8495 (t0) cc_final: 0.8255 (t0) REVERT: C 619 TYR cc_start: 0.8069 (t80) cc_final: 0.7701 (t80) outliers start: 14 outliers final: 4 residues processed: 143 average time/residue: 0.1332 time to fit residues: 28.9509 Evaluate side-chains 117 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 280 ASN ** A 630 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 = 0.3791 r_free = 0.3791 target = 0.099311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079215 restraints weight = 41610.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.081790 restraints weight = 24862.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.083344 restraints weight = 15341.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083643 restraints weight = 11516.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084227 restraints weight = 10761.798| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17057 Z= 0.125 Angle : 0.619 12.096 23334 Z= 0.285 Chirality : 0.046 0.256 2880 Planarity : 0.004 0.073 2776 Dihedral : 11.339 86.201 4176 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.88 % Allowed : 10.80 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.18), residues: 1872 helix: -1.21 (0.26), residues: 333 sheet: -1.76 (0.22), residues: 473 loop : -2.31 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 432 TYR 0.014 0.001 TYR C 638 PHE 0.012 0.001 PHE B 651 TRP 0.029 0.001 TRP F 35 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00282 (16921) covalent geometry : angle 0.58118 (22959) SS BOND : bond 0.00334 ( 33) SS BOND : angle 0.86664 ( 66) hydrogen bonds : bond 0.04557 ( 409) hydrogen bonds : angle 5.77293 ( 1152) link_ALPHA1-2 : bond 0.00620 ( 1) link_ALPHA1-2 : angle 1.77311 ( 3) link_ALPHA1-3 : bond 0.01004 ( 6) link_ALPHA1-3 : angle 2.09705 ( 18) link_ALPHA1-6 : bond 0.00862 ( 4) link_ALPHA1-6 : angle 1.80691 ( 12) link_BETA1-4 : bond 0.00513 ( 29) link_BETA1-4 : angle 1.78201 ( 87) link_NAG-ASN : bond 0.00336 ( 63) link_NAG-ASN : angle 1.96700 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8111 (p0) cc_final: 0.7852 (p0) REVERT: E 192 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7099 (ttm170) REVERT: G 302 MET cc_start: 0.8625 (mmt) cc_final: 0.8406 (mmt) REVERT: H 38 ARG cc_start: 0.7242 (ptt180) cc_final: 0.6863 (ptp-170) REVERT: H 51 ILE cc_start: 0.9076 (tt) cc_final: 0.8476 (mm) REVERT: H 64 TRP cc_start: 0.6562 (m-10) cc_final: 0.6314 (m-90) REVERT: H 91 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) REVERT: H 108 MET cc_start: 0.7975 (tpp) cc_final: 0.7717 (tpp) REVERT: C 607 ASN cc_start: 0.8464 (t0) cc_final: 0.8205 (t0) REVERT: C 619 TYR cc_start: 0.8119 (t80) cc_final: 0.7753 (t80) outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 0.1270 time to fit residues: 26.7924 Evaluate side-chains 120 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 655 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN F 246 GLN F 392 ASN G 280 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075705 restraints weight = 41850.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079092 restraints weight = 25631.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080440 restraints weight = 15256.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080998 restraints weight = 10981.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081222 restraints weight = 10894.250| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17057 Z= 0.248 Angle : 0.712 11.829 23334 Z= 0.331 Chirality : 0.049 0.273 2880 Planarity : 0.004 0.041 2776 Dihedral : 10.541 81.078 4176 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.83 % Allowed : 12.57 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.18), residues: 1872 helix: -0.87 (0.28), residues: 334 sheet: -1.73 (0.22), residues: 469 loop : -2.19 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 170 TYR 0.012 0.001 TYR C 638 PHE 0.018 0.002 PHE G 93 TRP 0.026 0.002 TRP C 571 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00576 (16921) covalent geometry : angle 0.67175 (22959) SS BOND : bond 0.00470 ( 33) SS BOND : angle 1.14397 ( 66) hydrogen bonds : bond 0.04508 ( 409) hydrogen bonds : angle 5.72030 ( 1152) link_ALPHA1-2 : bond 0.00436 ( 1) link_ALPHA1-2 : angle 1.69141 ( 3) link_ALPHA1-3 : bond 0.00977 ( 6) link_ALPHA1-3 : angle 2.24466 ( 18) link_ALPHA1-6 : bond 0.00810 ( 4) link_ALPHA1-6 : angle 1.73610 ( 12) link_BETA1-4 : bond 0.00494 ( 29) link_BETA1-4 : angle 1.77981 ( 87) link_NAG-ASN : bond 0.00405 ( 63) link_NAG-ASN : angle 2.26272 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 192 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7237 (ttm170) REVERT: G 125 LEU cc_start: 0.9292 (tp) cc_final: 0.9051 (tp) REVERT: H 38 ARG cc_start: 0.7301 (ptt180) cc_final: 0.6773 (ptp-170) REVERT: H 51 ILE cc_start: 0.9117 (tt) cc_final: 0.8557 (mm) REVERT: H 64 TRP cc_start: 0.6709 (m-10) cc_final: 0.6359 (m-90) REVERT: H 91 TYR cc_start: 0.7751 (m-80) cc_final: 0.7525 (m-80) REVERT: H 98 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: H 100 GLU cc_start: 0.8961 (pt0) cc_final: 0.8745 (pt0) REVERT: C 607 ASN cc_start: 0.8619 (t0) cc_final: 0.8279 (t0) REVERT: C 612 SER cc_start: 0.8775 (m) cc_final: 0.8294 (t) REVERT: C 619 TYR cc_start: 0.8236 (t80) cc_final: 0.7793 (t80) outliers start: 31 outliers final: 20 residues processed: 136 average time/residue: 0.1270 time to fit residues: 26.5319 Evaluate side-chains 127 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 125 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 ASN G 280 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.093702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073071 restraints weight = 42518.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075378 restraints weight = 23868.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076958 restraints weight = 16419.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077992 restraints weight = 12744.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.078686 restraints weight = 10740.849| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17057 Z= 0.137 Angle : 0.630 11.966 23334 Z= 0.290 Chirality : 0.046 0.265 2880 Planarity : 0.003 0.035 2776 Dihedral : 9.723 75.491 4176 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.18), residues: 1872 helix: -0.57 (0.29), residues: 334 sheet: -1.66 (0.22), residues: 472 loop : -2.04 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 46 TYR 0.013 0.001 TYR C 638 PHE 0.016 0.001 PHE L 32 TRP 0.036 0.001 TRP F 427 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00315 (16921) covalent geometry : angle 0.59079 (22959) SS BOND : bond 0.00365 ( 33) SS BOND : angle 0.93352 ( 66) hydrogen bonds : bond 0.03878 ( 409) hydrogen bonds : angle 5.34687 ( 1152) link_ALPHA1-2 : bond 0.00536 ( 1) link_ALPHA1-2 : angle 1.57871 ( 3) link_ALPHA1-3 : bond 0.01014 ( 6) link_ALPHA1-3 : angle 2.23204 ( 18) link_ALPHA1-6 : bond 0.01071 ( 4) link_ALPHA1-6 : angle 1.53673 ( 12) link_BETA1-4 : bond 0.00478 ( 29) link_BETA1-4 : angle 1.72364 ( 87) link_NAG-ASN : bond 0.00328 ( 63) link_NAG-ASN : angle 2.07183 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9097 (p) REVERT: F 302 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8164 (mmp) REVERT: E 170 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7540 (ttp80) REVERT: E 192 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: G 125 LEU cc_start: 0.9236 (tp) cc_final: 0.9002 (tp) REVERT: G 302 MET cc_start: 0.8621 (mmt) cc_final: 0.8366 (mmp) REVERT: H 38 ARG cc_start: 0.7338 (ptt180) cc_final: 0.6765 (ptp-170) REVERT: H 51 ILE cc_start: 0.9128 (tt) cc_final: 0.8536 (mm) REVERT: H 64 TRP cc_start: 0.6726 (m-10) cc_final: 0.6294 (m-10) REVERT: H 91 TYR cc_start: 0.7758 (m-80) cc_final: 0.7546 (m-80) REVERT: H 98 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: H 100 GLU cc_start: 0.8948 (pt0) cc_final: 0.8714 (pt0) REVERT: C 607 ASN cc_start: 0.8612 (t0) cc_final: 0.8274 (t0) REVERT: C 612 SER cc_start: 0.8779 (m) cc_final: 0.8278 (t) REVERT: C 619 TYR cc_start: 0.8219 (t80) cc_final: 0.7792 (t80) outliers start: 33 outliers final: 19 residues processed: 144 average time/residue: 0.1254 time to fit residues: 28.2144 Evaluate side-chains 133 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 129 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 ASN G 280 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.093789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073047 restraints weight = 43000.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075418 restraints weight = 24124.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.076999 restraints weight = 16645.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078035 restraints weight = 12974.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078738 restraints weight = 10918.328| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17057 Z= 0.106 Angle : 0.604 12.027 23334 Z= 0.276 Chirality : 0.046 0.261 2880 Planarity : 0.003 0.037 2776 Dihedral : 9.142 68.937 4176 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.77 % Allowed : 13.98 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.19), residues: 1872 helix: -0.28 (0.30), residues: 330 sheet: -1.58 (0.22), residues: 475 loop : -1.91 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 46 TYR 0.011 0.001 TYR L 36 PHE 0.011 0.001 PHE E 210 TRP 0.034 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00238 (16921) covalent geometry : angle 0.56583 (22959) SS BOND : bond 0.00328 ( 33) SS BOND : angle 0.84200 ( 66) hydrogen bonds : bond 0.03477 ( 409) hydrogen bonds : angle 5.05776 ( 1152) link_ALPHA1-2 : bond 0.00593 ( 1) link_ALPHA1-2 : angle 1.49139 ( 3) link_ALPHA1-3 : bond 0.01046 ( 6) link_ALPHA1-3 : angle 2.16093 ( 18) link_ALPHA1-6 : bond 0.01131 ( 4) link_ALPHA1-6 : angle 1.47194 ( 12) link_BETA1-4 : bond 0.00505 ( 29) link_BETA1-4 : angle 1.68150 ( 87) link_NAG-ASN : bond 0.00348 ( 63) link_NAG-ASN : angle 1.97865 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 97 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8341 (ptmt) REVERT: F 295 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9072 (p) REVERT: F 302 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8200 (mmp) REVERT: E 170 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7644 (ttp80) REVERT: H 38 ARG cc_start: 0.7367 (ptt180) cc_final: 0.6720 (ptp90) REVERT: H 51 ILE cc_start: 0.9115 (tt) cc_final: 0.8506 (mm) REVERT: H 64 TRP cc_start: 0.6724 (m-10) cc_final: 0.6245 (m-10) REVERT: H 98 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: H 100 GLU cc_start: 0.9013 (pt0) cc_final: 0.8788 (pt0) REVERT: C 607 ASN cc_start: 0.8579 (t0) cc_final: 0.8273 (t0) REVERT: C 612 SER cc_start: 0.8787 (m) cc_final: 0.8287 (t) REVERT: C 619 TYR cc_start: 0.8221 (t80) cc_final: 0.7799 (t80) REVERT: C 659 ASP cc_start: 0.5082 (m-30) cc_final: 0.4455 (p0) outliers start: 30 outliers final: 21 residues processed: 146 average time/residue: 0.1314 time to fit residues: 29.1746 Evaluate side-chains 137 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN F 425 ASN G 280 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071986 restraints weight = 42561.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073779 restraints weight = 29274.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075390 restraints weight = 18727.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075850 restraints weight = 13899.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076228 restraints weight = 12949.957| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 17057 Z= 0.332 Angle : 0.813 11.700 23334 Z= 0.379 Chirality : 0.051 0.293 2880 Planarity : 0.004 0.050 2776 Dihedral : 9.426 65.470 4176 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.77 % Allowed : 14.99 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1872 helix: -0.54 (0.29), residues: 334 sheet: -1.75 (0.22), residues: 496 loop : -1.98 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 273 TYR 0.014 0.002 TYR F 40 PHE 0.032 0.003 PHE H 67 TRP 0.058 0.002 TRP C 571 HIS 0.007 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00775 (16921) covalent geometry : angle 0.77308 (22959) SS BOND : bond 0.00546 ( 33) SS BOND : angle 1.34000 ( 66) hydrogen bonds : bond 0.04439 ( 409) hydrogen bonds : angle 5.57881 ( 1152) link_ALPHA1-2 : bond 0.00385 ( 1) link_ALPHA1-2 : angle 1.64033 ( 3) link_ALPHA1-3 : bond 0.00889 ( 6) link_ALPHA1-3 : angle 2.33639 ( 18) link_ALPHA1-6 : bond 0.01200 ( 4) link_ALPHA1-6 : angle 1.25911 ( 12) link_BETA1-4 : bond 0.00460 ( 29) link_BETA1-4 : angle 1.81208 ( 87) link_NAG-ASN : bond 0.00523 ( 63) link_NAG-ASN : angle 2.50662 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9088 (p) REVERT: E 290 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6854 (pp20) REVERT: G 125 LEU cc_start: 0.9331 (tp) cc_final: 0.9126 (tp) REVERT: H 38 ARG cc_start: 0.7317 (ptt180) cc_final: 0.6678 (ptp90) REVERT: H 51 ILE cc_start: 0.9204 (tt) cc_final: 0.8697 (mm) REVERT: H 64 TRP cc_start: 0.6413 (m-10) cc_final: 0.6104 (m-10) REVERT: H 98 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: H 108 MET cc_start: 0.7427 (tpp) cc_final: 0.7158 (tpp) REVERT: C 607 ASN cc_start: 0.8649 (t0) cc_final: 0.8210 (t0) REVERT: C 612 SER cc_start: 0.8931 (m) cc_final: 0.8485 (t) outliers start: 47 outliers final: 34 residues processed: 146 average time/residue: 0.1203 time to fit residues: 27.7147 Evaluate side-chains 140 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 128 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 ASN G 280 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070733 restraints weight = 44307.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073060 restraints weight = 25231.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074553 restraints weight = 17676.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075570 restraints weight = 14071.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.076201 restraints weight = 11964.996| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17057 Z= 0.136 Angle : 0.654 11.782 23334 Z= 0.301 Chirality : 0.046 0.279 2880 Planarity : 0.003 0.042 2776 Dihedral : 8.743 61.050 4176 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.83 % Allowed : 15.99 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.19), residues: 1872 helix: -0.22 (0.30), residues: 325 sheet: -1.52 (0.22), residues: 489 loop : -1.88 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 633 TYR 0.014 0.001 TYR C 638 PHE 0.030 0.002 PHE H 67 TRP 0.038 0.002 TRP C 571 HIS 0.003 0.001 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00313 (16921) covalent geometry : angle 0.61434 (22959) SS BOND : bond 0.00385 ( 33) SS BOND : angle 0.97085 ( 66) hydrogen bonds : bond 0.03694 ( 409) hydrogen bonds : angle 5.16095 ( 1152) link_ALPHA1-2 : bond 0.00560 ( 1) link_ALPHA1-2 : angle 1.50083 ( 3) link_ALPHA1-3 : bond 0.00928 ( 6) link_ALPHA1-3 : angle 2.08823 ( 18) link_ALPHA1-6 : bond 0.01279 ( 4) link_ALPHA1-6 : angle 1.47150 ( 12) link_BETA1-4 : bond 0.00488 ( 29) link_BETA1-4 : angle 1.74277 ( 87) link_NAG-ASN : bond 0.00337 ( 63) link_NAG-ASN : angle 2.14954 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9071 (p) REVERT: E 170 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7566 (ttp80) REVERT: E 258 GLN cc_start: 0.8270 (mt0) cc_final: 0.8050 (mt0) REVERT: E 290 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: H 38 ARG cc_start: 0.7333 (ptt180) cc_final: 0.6818 (ptp-170) REVERT: H 51 ILE cc_start: 0.9157 (tt) cc_final: 0.8535 (mm) REVERT: H 100 GLU cc_start: 0.8898 (pt0) cc_final: 0.8685 (pt0) REVERT: H 108 MET cc_start: 0.7904 (tpp) cc_final: 0.7674 (tpp) REVERT: L 46 LEU cc_start: 0.8648 (pt) cc_final: 0.8021 (tt) REVERT: C 607 ASN cc_start: 0.8677 (t0) cc_final: 0.8249 (t0) REVERT: C 612 SER cc_start: 0.8894 (m) cc_final: 0.8384 (t) outliers start: 31 outliers final: 23 residues processed: 144 average time/residue: 0.1222 time to fit residues: 27.0987 Evaluate side-chains 136 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 280 ASN ** A 630 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 = 0.3668 r_free = 0.3668 target = 0.092030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070763 restraints weight = 44587.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073115 restraints weight = 25415.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.074677 restraints weight = 17767.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075700 restraints weight = 14021.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076380 restraints weight = 11927.171| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17057 Z= 0.144 Angle : 0.652 11.722 23334 Z= 0.300 Chirality : 0.046 0.278 2880 Planarity : 0.003 0.044 2776 Dihedral : 8.371 61.394 4176 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.95 % Allowed : 15.99 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.19), residues: 1872 helix: -0.09 (0.30), residues: 331 sheet: -1.46 (0.23), residues: 477 loop : -1.83 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 633 TYR 0.014 0.001 TYR C 638 PHE 0.025 0.002 PHE H 67 TRP 0.042 0.001 TRP C 571 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00333 (16921) covalent geometry : angle 0.61360 (22959) SS BOND : bond 0.00369 ( 33) SS BOND : angle 0.95673 ( 66) hydrogen bonds : bond 0.03524 ( 409) hydrogen bonds : angle 5.02811 ( 1152) link_ALPHA1-2 : bond 0.00569 ( 1) link_ALPHA1-2 : angle 1.46815 ( 3) link_ALPHA1-3 : bond 0.00915 ( 6) link_ALPHA1-3 : angle 1.92088 ( 18) link_ALPHA1-6 : bond 0.01376 ( 4) link_ALPHA1-6 : angle 1.98207 ( 12) link_BETA1-4 : bond 0.00486 ( 29) link_BETA1-4 : angle 1.71425 ( 87) link_NAG-ASN : bond 0.00330 ( 63) link_NAG-ASN : angle 2.12227 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9068 (p) REVERT: E 170 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: E 258 GLN cc_start: 0.8275 (mt0) cc_final: 0.8062 (mt0) REVERT: E 290 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6860 (pp20) REVERT: H 38 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6503 (ptp-170) REVERT: H 51 ILE cc_start: 0.9157 (tt) cc_final: 0.8532 (mm) REVERT: L 46 LEU cc_start: 0.8651 (pt) cc_final: 0.8070 (tt) REVERT: L 47 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8047 (mm) REVERT: C 607 ASN cc_start: 0.8684 (t0) cc_final: 0.8272 (t0) REVERT: C 612 SER cc_start: 0.8892 (m) cc_final: 0.8382 (t) REVERT: C 659 ASP cc_start: 0.4930 (m-30) cc_final: 0.4309 (p0) outliers start: 33 outliers final: 26 residues processed: 150 average time/residue: 0.1132 time to fit residues: 26.6580 Evaluate side-chains 141 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 ASN G 280 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069397 restraints weight = 44263.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071545 restraints weight = 26361.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072980 restraints weight = 18835.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073904 restraints weight = 15075.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.074528 restraints weight = 12996.221| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17057 Z= 0.244 Angle : 0.737 11.398 23334 Z= 0.340 Chirality : 0.049 0.291 2880 Planarity : 0.004 0.044 2776 Dihedral : 8.513 64.576 4176 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.95 % Allowed : 16.17 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.19), residues: 1872 helix: -0.19 (0.30), residues: 331 sheet: -1.43 (0.23), residues: 477 loop : -1.90 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 46 TYR 0.015 0.001 TYR C 638 PHE 0.022 0.002 PHE H 67 TRP 0.036 0.002 TRP F 69 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00570 (16921) covalent geometry : angle 0.69732 (22959) SS BOND : bond 0.00453 ( 33) SS BOND : angle 1.16859 ( 66) hydrogen bonds : bond 0.03924 ( 409) hydrogen bonds : angle 5.22786 ( 1152) link_ALPHA1-2 : bond 0.00482 ( 1) link_ALPHA1-2 : angle 1.53072 ( 3) link_ALPHA1-3 : bond 0.00802 ( 6) link_ALPHA1-3 : angle 1.90848 ( 18) link_ALPHA1-6 : bond 0.01201 ( 4) link_ALPHA1-6 : angle 1.96428 ( 12) link_BETA1-4 : bond 0.00468 ( 29) link_BETA1-4 : angle 1.77506 ( 87) link_NAG-ASN : bond 0.00394 ( 63) link_NAG-ASN : angle 2.33145 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9065 (p) REVERT: E 290 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: H 38 ARG cc_start: 0.7362 (ptt180) cc_final: 0.6602 (ptp90) REVERT: H 64 TRP cc_start: 0.6652 (m-10) cc_final: 0.6213 (m-10) REVERT: H 100 GLU cc_start: 0.8838 (pt0) cc_final: 0.8401 (pt0) REVERT: L 46 LEU cc_start: 0.8631 (pt) cc_final: 0.7990 (tt) REVERT: C 607 ASN cc_start: 0.8638 (t0) cc_final: 0.8189 (t0) REVERT: C 612 SER cc_start: 0.8884 (m) cc_final: 0.8389 (t) outliers start: 33 outliers final: 28 residues processed: 141 average time/residue: 0.1200 time to fit residues: 26.7346 Evaluate side-chains 136 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 81 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069557 restraints weight = 44375.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072717 restraints weight = 28076.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073556 restraints weight = 17722.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074011 restraints weight = 14445.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074127 restraints weight = 12999.389| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 17057 Z= 0.244 Angle : 0.898 59.194 23334 Z= 0.466 Chirality : 0.050 0.626 2880 Planarity : 0.004 0.047 2776 Dihedral : 8.545 64.494 4176 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.00 % Rotamer: Outliers : 1.77 % Allowed : 16.34 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1872 helix: -0.17 (0.30), residues: 331 sheet: -1.43 (0.23), residues: 477 loop : -1.90 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 170 TYR 0.012 0.001 TYR C 638 PHE 0.019 0.002 PHE H 67 TRP 0.029 0.002 TRP L 35 HIS 0.004 0.001 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00544 (16921) covalent geometry : angle 0.86847 (22959) SS BOND : bond 0.00419 ( 33) SS BOND : angle 1.17325 ( 66) hydrogen bonds : bond 0.03855 ( 409) hydrogen bonds : angle 5.22354 ( 1152) link_ALPHA1-2 : bond 0.00502 ( 1) link_ALPHA1-2 : angle 1.52940 ( 3) link_ALPHA1-3 : bond 0.00808 ( 6) link_ALPHA1-3 : angle 1.91954 ( 18) link_ALPHA1-6 : bond 0.01196 ( 4) link_ALPHA1-6 : angle 1.97495 ( 12) link_BETA1-4 : bond 0.00453 ( 29) link_BETA1-4 : angle 1.77376 ( 87) link_NAG-ASN : bond 0.00382 ( 63) link_NAG-ASN : angle 2.33304 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.90 seconds wall clock time: 41 minutes 57.47 seconds (2517.47 seconds total)