Starting phenix.real_space_refine on Sat Feb 7 21:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5w_39786/02_2026/8z5w_39786.cif" } resolution = 3.46 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= -0.002 sd= 0.073 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 178 5.16 5 C 22346 2.51 5 N 6311 2.21 5 O 7293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36128 Number of models: 1 Model: "" Number of chains: 39 Chain: "0" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1361 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 12, 'TRANS': 167} Chain: "9" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1361 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 12, 'TRANS': 167} Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1956 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "AA" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AB" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AC" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "AD" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AE" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AF" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 158 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "AG" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AH" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AI" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AJ" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 163 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Chain: "AK" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 169 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 4, 'TRANS': 20} Chain: "AL" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "AM" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 224 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "AN" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 224 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "AO" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "B" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1956 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1956 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "AP" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1956 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "AQ" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1956 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "AR" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1858 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 Chain: "b" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "c" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 835 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "d" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "e" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "f" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "g" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "h" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "i" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "j" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "k" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "l" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "m" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "n" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "o" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "p" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "q" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Time building chain proxies: 8.26, per 1000 atoms: 0.23 Number of scatterers: 36128 At special positions: 0 Unit cell: (138, 144, 190.8, 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 178 16.00 O 7293 8.00 N 6311 7.00 C 22346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8750 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 115 sheets defined 33.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain '0' and resid 26 through 31 removed outlier: 3.540A pdb=" N GLY 0 29 " --> pdb=" O SER 0 26 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR 0 31 " --> pdb=" O PHE 0 28 " (cutoff:3.500A) Processing helix chain '9' and resid 23 through 29 removed outlier: 3.643A pdb=" N GLY 9 29 " --> pdb=" O TYR 9 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 28 removed outlier: 3.555A pdb=" N TRP A 6 " --> pdb=" O HIS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 226 through 262 Processing helix chain 'AF' and resid 349 through 355 removed outlier: 3.864A pdb=" N VALAF 353 " --> pdb=" O ILEAF 349 " (cutoff:3.500A) Processing helix chain 'AK' and resid 343 through 347 Processing helix chain 'AL' and resid 350 through 357 removed outlier: 3.569A pdb=" N LYSAL 357 " --> pdb=" O VALAL 353 " (cutoff:3.500A) Processing helix chain 'AM' and resid 343 through 347 Processing helix chain 'AM' and resid 350 through 359 removed outlier: 4.122A pdb=" N ASPAM 358 " --> pdb=" O ALAAM 354 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYAM 359 " --> pdb=" O GLNAM 355 " (cutoff:3.500A) Processing helix chain 'AN' and resid 337 through 342 removed outlier: 3.514A pdb=" N ASNAN 341 " --> pdb=" O GLYAN 337 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLNAN 342 " --> pdb=" O ALAAN 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 337 through 342' Processing helix chain 'AN' and resid 343 through 347 Processing helix chain 'AN' and resid 350 through 355 Processing helix chain 'AN' and resid 356 through 358 No H-bonds generated for 'chain 'AN' and resid 356 through 358' Processing helix chain 'AO' and resid 350 through 357 removed outlier: 3.573A pdb=" N METAO 356 " --> pdb=" O ASPAO 352 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYSAO 357 " --> pdb=" O VALAO 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 28 removed outlier: 3.617A pdb=" N TRP B 6 " --> pdb=" O HIS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 226 through 262 removed outlier: 3.811A pdb=" N LEU B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 28 removed outlier: 3.627A pdb=" N GLY C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 226 through 262 removed outlier: 3.510A pdb=" N ASN C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing helix chain 'AP' and resid 2 through 28 removed outlier: 3.702A pdb=" N TRPAP 6 " --> pdb=" O HISAP 2 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLYAP 11 " --> pdb=" O VALAP 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASNAP 25 " --> pdb=" O THRAP 21 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEUAP 26 " --> pdb=" O ILEAP 22 " (cutoff:3.500A) Processing helix chain 'AP' and resid 62 through 65 Processing helix chain 'AP' and resid 181 through 185 Processing helix chain 'AP' and resid 226 through 262 removed outlier: 3.500A pdb=" N ILEAP 248 " --> pdb=" O ASNAP 244 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 2 through 28 removed outlier: 3.713A pdb=" N TRPAQ 6 " --> pdb=" O HISAQ 2 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYAQ 11 " --> pdb=" O VALAQ 7 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 62 through 65 Processing helix chain 'AQ' and resid 181 through 185 Processing helix chain 'AQ' and resid 226 through 262 removed outlier: 3.652A pdb=" N ASNAQ 259 " --> pdb=" O METAQ 255 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 28 Processing helix chain 'AR' and resid 181 through 185 Processing helix chain 'AR' and resid 226 through 262 removed outlier: 3.507A pdb=" N VALAR 247 " --> pdb=" O METAR 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 10 Processing helix chain 'b' and resid 11 through 32 removed outlier: 3.809A pdb=" N VAL b 16 " --> pdb=" O HIS b 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY b 17 " --> pdb=" O GLN b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 54 Processing helix chain 'b' and resid 95 through 130 removed outlier: 3.541A pdb=" N ASN b 101 " --> pdb=" O ASP b 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 10 Processing helix chain 'c' and resid 11 through 32 removed outlier: 3.911A pdb=" N VAL c 16 " --> pdb=" O HIS c 12 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY c 17 " --> pdb=" O GLN c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 53 removed outlier: 3.641A pdb=" N GLU c 48 " --> pdb=" O ASP c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 130 removed outlier: 3.503A pdb=" N ASN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE c 121 " --> pdb=" O LEU c 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 10 Processing helix chain 'd' and resid 11 through 32 removed outlier: 3.787A pdb=" N VAL d 16 " --> pdb=" O HIS d 12 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY d 17 " --> pdb=" O GLN d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 54 Processing helix chain 'd' and resid 95 through 130 removed outlier: 3.821A pdb=" N ASN d 101 " --> pdb=" O ASP d 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 9 Processing helix chain 'e' and resid 11 through 32 removed outlier: 3.591A pdb=" N VAL e 16 " --> pdb=" O HIS e 12 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY e 17 " --> pdb=" O GLN e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 54 Processing helix chain 'e' and resid 95 through 130 removed outlier: 3.561A pdb=" N PHE e 121 " --> pdb=" O LEU e 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 10 Processing helix chain 'f' and resid 11 through 32 removed outlier: 3.782A pdb=" N VAL f 16 " --> pdb=" O HIS f 12 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY f 17 " --> pdb=" O GLN f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 54 Processing helix chain 'f' and resid 95 through 130 removed outlier: 3.521A pdb=" N PHE f 121 " --> pdb=" O LEU f 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 30 Processing helix chain 'g' and resid 100 through 134 removed outlier: 3.508A pdb=" N GLN g 127 " --> pdb=" O ASP g 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN g 134 " --> pdb=" O LEU g 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 30 removed outlier: 3.517A pdb=" N PHE h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 134 removed outlier: 3.526A pdb=" N ASN h 118 " --> pdb=" O ALA h 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL h 119 " --> pdb=" O TYR h 115 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN h 134 " --> pdb=" O LEU h 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 29 removed outlier: 3.834A pdb=" N PHE i 7 " --> pdb=" O LEU i 3 " (cutoff:3.500A) Processing helix chain 'i' and resid 100 through 135 removed outlier: 3.505A pdb=" N VAL i 119 " --> pdb=" O TYR i 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL i 121 " --> pdb=" O THR i 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 30 removed outlier: 3.664A pdb=" N PHE j 7 " --> pdb=" O LEU j 3 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 134 removed outlier: 3.573A pdb=" N VAL j 119 " --> pdb=" O TYR j 115 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL j 121 " --> pdb=" O THR j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 30 removed outlier: 3.673A pdb=" N ASN k 8 " --> pdb=" O PHE k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 134 removed outlier: 3.538A pdb=" N ALA k 106 " --> pdb=" O MET k 102 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL k 119 " --> pdb=" O TYR k 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 30 Processing helix chain 'l' and resid 100 through 134 Processing helix chain 'm' and resid 3 through 28 removed outlier: 3.527A pdb=" N ASN m 25 " --> pdb=" O LEU m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 154 through 158 removed outlier: 4.080A pdb=" N PHE m 158 " --> pdb=" O ALA m 155 " (cutoff:3.500A) Processing helix chain 'm' and resid 170 through 172 No H-bonds generated for 'chain 'm' and resid 170 through 172' Processing helix chain 'm' and resid 210 through 243 removed outlier: 3.853A pdb=" N ARG m 223 " --> pdb=" O ILE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 244 through 247 Processing helix chain 'n' and resid 3 through 28 removed outlier: 3.538A pdb=" N GLY n 11 " --> pdb=" O LEU n 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN n 14 " --> pdb=" O SER n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 170 through 172 No H-bonds generated for 'chain 'n' and resid 170 through 172' Processing helix chain 'n' and resid 210 through 242 removed outlier: 3.888A pdb=" N ASP n 220 " --> pdb=" O THR n 216 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG n 223 " --> pdb=" O ILE n 219 " (cutoff:3.500A) Processing helix chain 'n' and resid 243 through 246 removed outlier: 3.999A pdb=" N LEU n 246 " --> pdb=" O ASP n 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 243 through 246' Processing helix chain 'o' and resid 3 through 28 removed outlier: 3.748A pdb=" N GLY o 11 " --> pdb=" O LEU o 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) Processing helix chain 'o' and resid 170 through 172 No H-bonds generated for 'chain 'o' and resid 170 through 172' Processing helix chain 'o' and resid 210 through 243 removed outlier: 3.754A pdb=" N ASP o 220 " --> pdb=" O THR o 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 28 removed outlier: 3.582A pdb=" N GLY p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 154 through 158 removed outlier: 4.117A pdb=" N PHE p 158 " --> pdb=" O ALA p 155 " (cutoff:3.500A) Processing helix chain 'p' and resid 170 through 172 No H-bonds generated for 'chain 'p' and resid 170 through 172' Processing helix chain 'p' and resid 210 through 244 removed outlier: 3.723A pdb=" N LYS p 230 " --> pdb=" O GLU p 226 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER p 241 " --> pdb=" O GLU p 237 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER p 244 " --> pdb=" O LYS p 240 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 248 removed outlier: 4.183A pdb=" N MET p 248 " --> pdb=" O LEU p 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 245 through 248' Processing helix chain 'q' and resid 3 through 28 removed outlier: 3.506A pdb=" N GLY q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN q 25 " --> pdb=" O LEU q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 170 through 172 No H-bonds generated for 'chain 'q' and resid 170 through 172' Processing helix chain 'q' and resid 210 through 242 Processing helix chain 'q' and resid 243 through 247 removed outlier: 3.777A pdb=" N LEU q 246 " --> pdb=" O ASP q 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 37 through 38 removed outlier: 6.971A pdb=" N LEU 0 37 " --> pdb=" O ASN 0 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU 0 57 " --> pdb=" O GLU 0 78 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU 0 77 " --> pdb=" O ASN 0 98 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA 0 97 " --> pdb=" O ASN 0 118 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU 0 117 " --> pdb=" O SER 0 138 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU 0 137 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU 0 157 " --> pdb=" O PHE 0 178 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE 0 177 " --> pdb=" O ALA 0 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '0' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain '0' and resid 132 through 133 removed outlier: 4.172A pdb=" N THR 0 192 " --> pdb=" O MET 0 171 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL 0 173 " --> pdb=" O THR 0 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9' and resid 37 through 38 removed outlier: 6.632A pdb=" N LEU 9 37 " --> pdb=" O ASN 9 58 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU 9 57 " --> pdb=" O GLU 9 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU 9 77 " --> pdb=" O ASN 9 98 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA 9 97 " --> pdb=" O ASN 9 118 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU 9 117 " --> pdb=" O SER 9 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU 9 137 " --> pdb=" O TYR 9 158 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU 9 157 " --> pdb=" O PHE 9 178 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE 9 177 " --> pdb=" O ALA 9 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain '9' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain '9' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'A' and resid 37 through 43 removed outlier: 3.765A pdb=" N ALA A 76 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 42 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL A 74 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AB1, first strand: chain 'A' and resid 95 through 98 Processing sheet with id=AB2, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AB4, first strand: chain 'A' and resid 147 through 152 removed outlier: 4.131A pdb=" N SER A 149 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 172 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 160 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 170 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.562A pdb=" N GLY A 205 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'AA' and resid 339 through 340 removed outlier: 4.246A pdb=" N LEU b 79 " --> pdb=" O GLY b 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'AB' and resid 339 through 340 Processing sheet with id=AB9, first strand: chain 'AC' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'AD' and resid 339 through 340 Processing sheet with id=AC2, first strand: chain 'AE' and resid 339 through 340 Processing sheet with id=AC3, first strand: chain 'AK' and resid 331 through 334 removed outlier: 3.522A pdb=" N ALA g 51 " --> pdb=" O VALAK 332 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY g 69 " --> pdb=" O VAL g 48 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY g 50 " --> pdb=" O VAL g 67 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL g 67 " --> pdb=" O GLY g 50 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU g 52 " --> pdb=" O VAL g 65 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL g 65 " --> pdb=" O GLU g 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AL' and resid 332 through 334 removed outlier: 4.145A pdb=" N GLY h 69 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY h 50 " --> pdb=" O VAL h 67 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL h 67 " --> pdb=" O GLY h 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AM' and resid 332 through 334 removed outlier: 4.426A pdb=" N GLY l 69 " --> pdb=" O VAL l 48 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY l 50 " --> pdb=" O VAL l 67 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL l 67 " --> pdb=" O GLY l 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'AN' and resid 332 through 334 removed outlier: 4.434A pdb=" N GLY j 69 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY j 50 " --> pdb=" O VAL j 67 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL j 67 " --> pdb=" O GLY j 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'AO' and resid 331 through 334 removed outlier: 4.357A pdb=" N GLY k 69 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY k 50 " --> pdb=" O VAL k 67 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL k 67 " --> pdb=" O GLY k 50 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLU k 52 " --> pdb=" O VAL k 65 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL k 65 " --> pdb=" O GLU k 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 37 through 43 removed outlier: 3.831A pdb=" N ALA B 76 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 42 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL B 74 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AD2, first strand: chain 'B' and resid 95 through 98 Processing sheet with id=AD3, first strand: chain 'B' and resid 112 through 115 removed outlier: 4.591A pdb=" N GLN B 104 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AD5, first strand: chain 'B' and resid 147 through 152 removed outlier: 3.923A pdb=" N SER B 149 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 158 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AD7, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.607A pdb=" N ALA C 76 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU C 42 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL C 74 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AE1, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AE2, first strand: chain 'C' and resid 95 through 98 Processing sheet with id=AE3, first strand: chain 'C' and resid 103 through 106 Processing sheet with id=AE4, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AE5, first strand: chain 'C' and resid 147 through 152 removed outlier: 6.437A pdb=" N ARG C 161 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE C 150 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER C 159 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL C 152 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU C 157 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 158 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AE7, first strand: chain 'AP' and resid 37 through 43 removed outlier: 3.687A pdb=" N ALAAP 76 " --> pdb=" O VALAP 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLUAP 42 " --> pdb=" O VALAP 74 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VALAP 74 " --> pdb=" O GLUAP 42 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'AP' and resid 47 through 48 Processing sheet with id=AE9, first strand: chain 'AP' and resid 86 through 88 Processing sheet with id=AF1, first strand: chain 'AP' and resid 95 through 98 removed outlier: 3.582A pdb=" N GLUAP 214 " --> pdb=" O GLUAP 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AP' and resid 103 through 106 Processing sheet with id=AF3, first strand: chain 'AP' and resid 120 through 122 Processing sheet with id=AF4, first strand: chain 'AP' and resid 149 through 152 removed outlier: 3.978A pdb=" N SERAP 149 " --> pdb=" O ARGAP 161 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VALAP 158 " --> pdb=" O VALAP 171 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'AP' and resid 176 through 178 Processing sheet with id=AF6, first strand: chain 'AP' and resid 186 through 189 removed outlier: 6.092A pdb=" N LEUAP 192 " --> pdb=" O ILEAP 188 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'AQ' and resid 37 through 43 removed outlier: 5.297A pdb=" N ARGAQ 38 " --> pdb=" O THRAQ 77 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THRAQ 77 " --> pdb=" O ARGAQ 38 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VALAQ 40 " --> pdb=" O VALAQ 75 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'AQ' and resid 46 through 48 Processing sheet with id=AF9, first strand: chain 'AQ' and resid 86 through 88 Processing sheet with id=AG1, first strand: chain 'AQ' and resid 95 through 98 removed outlier: 3.532A pdb=" N GLUAQ 214 " --> pdb=" O GLUAQ 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'AQ' and resid 137 through 138 removed outlier: 4.590A pdb=" N GLNAQ 104 " --> pdb=" O GLUAQ 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'AQ' and resid 137 through 138 removed outlier: 4.590A pdb=" N GLNAQ 104 " --> pdb=" O GLUAQ 138 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEUAQ 192 " --> pdb=" O ILEAQ 188 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'AQ' and resid 120 through 122 Processing sheet with id=AG5, first strand: chain 'AQ' and resid 147 through 152 removed outlier: 4.036A pdb=" N SERAQ 149 " --> pdb=" O ARGAQ 161 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VALAQ 158 " --> pdb=" O VALAQ 171 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VALAQ 162 " --> pdb=" O ASPAQ 167 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASPAQ 167 " --> pdb=" O VALAQ 162 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'AR' and resid 37 through 43 removed outlier: 3.893A pdb=" N ALAAR 76 " --> pdb=" O VALAR 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLUAR 42 " --> pdb=" O VALAR 74 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VALAR 74 " --> pdb=" O GLUAR 42 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'AR' and resid 47 through 48 Processing sheet with id=AG8, first strand: chain 'AR' and resid 86 through 88 Processing sheet with id=AG9, first strand: chain 'AR' and resid 95 through 98 removed outlier: 3.802A pdb=" N GLUAR 214 " --> pdb=" O GLUAR 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'AR' and resid 137 through 138 removed outlier: 4.584A pdb=" N GLNAR 104 " --> pdb=" O GLUAR 138 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'AR' and resid 137 through 138 removed outlier: 4.584A pdb=" N GLNAR 104 " --> pdb=" O GLUAR 138 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'AR' and resid 120 through 122 Processing sheet with id=AH4, first strand: chain 'AR' and resid 147 through 152 removed outlier: 3.964A pdb=" N SERAR 149 " --> pdb=" O ARGAR 161 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VALAR 158 " --> pdb=" O VALAR 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 78 through 81 Processing sheet with id=AH6, first strand: chain 'h' and resid 35 through 36 removed outlier: 7.220A pdb=" N SER h 35 " --> pdb=" O SER o 43 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLN o 45 " --> pdb=" O SER h 35 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 78 through 81 Processing sheet with id=AH8, first strand: chain 'i' and resid 35 through 36 removed outlier: 7.529A pdb=" N SER i 35 " --> pdb=" O SER n 43 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLN n 45 " --> pdb=" O SER i 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'i' and resid 45 through 51 removed outlier: 3.831A pdb=" N VAL i 48 " --> pdb=" O GLY i 69 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY i 69 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY i 50 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL i 67 " --> pdb=" O GLY i 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'i' and resid 78 through 81 Processing sheet with id=AI2, first strand: chain 'j' and resid 33 through 36 removed outlier: 6.346A pdb=" N ALA m 41 " --> pdb=" O SER j 33 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'j' and resid 78 through 81 Processing sheet with id=AI4, first strand: chain 'k' and resid 35 through 36 removed outlier: 7.237A pdb=" N SER k 35 " --> pdb=" O SER p 43 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLN p 45 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'k' and resid 78 through 81 Processing sheet with id=AI6, first strand: chain 'l' and resid 35 through 36 removed outlier: 3.674A pdb=" N SER q 43 " --> pdb=" O SER l 35 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'l' and resid 78 through 81 Processing sheet with id=AI8, first strand: chain 'm' and resid 71 through 73 Processing sheet with id=AI9, first strand: chain 'm' and resid 80 through 83 removed outlier: 4.665A pdb=" N SER m 198 " --> pdb=" O GLU m 83 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AJ2, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AJ3, first strand: chain 'm' and resid 105 through 107 Processing sheet with id=AJ4, first strand: chain 'm' and resid 135 through 140 removed outlier: 3.907A pdb=" N LYS m 137 " --> pdb=" O LEU m 149 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP m 162 " --> pdb=" O ILE m 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL m 148 " --> pdb=" O ALA m 160 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA m 160 " --> pdb=" O VAL m 148 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'm' and resid 174 through 176 Processing sheet with id=AJ6, first strand: chain 'n' and resid 36 through 37 removed outlier: 3.725A pdb=" N ALA n 36 " --> pdb=" O ASN n 65 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'n' and resid 71 through 73 Processing sheet with id=AJ8, first strand: chain 'n' and resid 80 through 83 removed outlier: 4.613A pdb=" N SER n 198 " --> pdb=" O GLU n 83 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AK1, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AK2, first strand: chain 'n' and resid 106 through 107 Processing sheet with id=AK3, first strand: chain 'n' and resid 135 through 140 removed outlier: 3.745A pdb=" N LYS n 137 " --> pdb=" O LEU n 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP n 162 " --> pdb=" O ILE n 146 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL n 148 " --> pdb=" O ALA n 160 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA n 160 " --> pdb=" O VAL n 148 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'n' and resid 174 through 176 Processing sheet with id=AK5, first strand: chain 'o' and resid 71 through 73 Processing sheet with id=AK6, first strand: chain 'o' and resid 82 through 83 removed outlier: 4.774A pdb=" N SER o 198 " --> pdb=" O GLU o 83 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AK8, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AK9, first strand: chain 'o' and resid 105 through 107 Processing sheet with id=AL1, first strand: chain 'o' and resid 135 through 140 removed outlier: 3.801A pdb=" N LYS o 137 " --> pdb=" O LEU o 149 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP o 162 " --> pdb=" O ILE o 146 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL o 148 " --> pdb=" O ALA o 160 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA o 160 " --> pdb=" O VAL o 148 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'o' and resid 174 through 176 Processing sheet with id=AL3, first strand: chain 'p' and resid 71 through 73 Processing sheet with id=AL4, first strand: chain 'p' and resid 80 through 83 removed outlier: 4.820A pdb=" N SER p 198 " --> pdb=" O GLU p 83 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AL6, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AL7, first strand: chain 'p' and resid 106 through 107 Processing sheet with id=AL8, first strand: chain 'p' and resid 135 through 140 removed outlier: 6.308A pdb=" N LEU p 149 " --> pdb=" O SER p 136 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE p 138 " --> pdb=" O SER p 147 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER p 147 " --> pdb=" O ILE p 138 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE p 140 " --> pdb=" O THR p 145 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR p 145 " --> pdb=" O ILE p 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP p 162 " --> pdb=" O ILE p 146 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL p 148 " --> pdb=" O ALA p 160 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA p 160 " --> pdb=" O VAL p 148 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'p' and resid 174 through 176 Processing sheet with id=AM1, first strand: chain 'q' and resid 71 through 73 Processing sheet with id=AM2, first strand: chain 'q' and resid 80 through 83 removed outlier: 3.564A pdb=" N THR q 81 " --> pdb=" O GLN q 200 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER q 198 " --> pdb=" O GLU q 83 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AM4, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AM5, first strand: chain 'q' and resid 105 through 107 Processing sheet with id=AM6, first strand: chain 'q' and resid 135 through 140 removed outlier: 3.795A pdb=" N LYS q 137 " --> pdb=" O LEU q 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP q 162 " --> pdb=" O ILE q 146 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL q 148 " --> pdb=" O ALA q 160 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA q 160 " --> pdb=" O VAL q 148 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'q' and resid 174 through 176 1619 hydrogen bonds defined for protein. 4590 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: 7.90 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6537 1.32 - 1.44: 8586 1.44 - 1.57: 21176 1.57 - 1.69: 0 1.69 - 1.81: 356 Bond restraints: 36655 Sorted by residual: bond pdb=" C PHE b 5 " pdb=" O PHE b 5 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" C PROAI 343 " pdb=" O PROAI 343 " ideal model delta sigma weight residual 1.240 1.207 0.034 1.12e-02 7.97e+03 9.03e+00 bond pdb=" N ASPAL 358 " pdb=" CA ASPAL 358 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.92e+00 bond pdb=" C PHE p 225 " pdb=" O PHE p 225 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.32e-02 5.74e+03 8.63e+00 bond pdb=" C PROAF 343 " pdb=" O PROAF 343 " ideal model delta sigma weight residual 1.240 1.208 0.032 1.12e-02 7.97e+03 8.25e+00 ... (remaining 36650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 49213 2.47 - 4.94: 423 4.94 - 7.40: 27 7.40 - 9.87: 2 9.87 - 12.34: 2 Bond angle restraints: 49667 Sorted by residual: angle pdb=" N MET p 227 " pdb=" CA MET p 227 " pdb=" C MET p 227 " ideal model delta sigma weight residual 113.41 103.49 9.92 1.22e+00 6.72e-01 6.61e+01 angle pdb=" C ARGAP 161 " pdb=" CA ARGAP 161 " pdb=" CB ARGAP 161 " ideal model delta sigma weight residual 109.75 97.41 12.34 1.65e+00 3.67e-01 5.59e+01 angle pdb=" CA GLN B 166 " pdb=" C GLN B 166 " pdb=" O GLN B 166 " ideal model delta sigma weight residual 121.72 115.91 5.81 1.18e+00 7.18e-01 2.42e+01 angle pdb=" CA SER i 37 " pdb=" C SER i 37 " pdb=" O SER i 37 " ideal model delta sigma weight residual 121.56 116.26 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" C GLNAF 351 " pdb=" N ASPAF 352 " pdb=" CA ASPAF 352 " ideal model delta sigma weight residual 120.58 112.51 8.07 1.71e+00 3.42e-01 2.23e+01 ... (remaining 49662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 21143 17.97 - 35.95: 930 35.95 - 53.92: 195 53.92 - 71.89: 69 71.89 - 89.87: 20 Dihedral angle restraints: 22357 sinusoidal: 8746 harmonic: 13611 Sorted by residual: dihedral pdb=" C ARGAP 161 " pdb=" N ARGAP 161 " pdb=" CA ARGAP 161 " pdb=" CB ARGAP 161 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" CD ARGAP 161 " pdb=" NE ARGAP 161 " pdb=" CZ ARGAP 161 " pdb=" NH1 ARGAP 161 " ideal model delta sinusoidal sigma weight residual 0.00 -37.68 37.68 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" C PROAF 343 " pdb=" N PROAF 343 " pdb=" CA PROAF 343 " pdb=" CB PROAF 343 " ideal model delta harmonic sigma weight residual -120.70 -112.54 -8.16 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 22354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4576 0.045 - 0.090: 778 0.090 - 0.135: 324 0.135 - 0.180: 9 0.180 - 0.225: 11 Chirality restraints: 5698 Sorted by residual: chirality pdb=" CA VALAK 332 " pdb=" N VALAK 332 " pdb=" C VALAK 332 " pdb=" CB VALAK 332 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLN B 165 " pdb=" N GLN B 165 " pdb=" C GLN B 165 " pdb=" CB GLN B 165 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA MET p 227 " pdb=" N MET p 227 " pdb=" C MET p 227 " pdb=" CB MET p 227 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5695 not shown) Planarity restraints: 6655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGAP 161 " 0.644 9.50e-02 1.11e+02 2.89e-01 5.10e+01 pdb=" NE ARGAP 161 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARGAP 161 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARGAP 161 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARGAP 161 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAL 357 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LYSAL 357 " -0.072 2.00e-02 2.50e+03 pdb=" O LYSAL 357 " 0.026 2.00e-02 2.50e+03 pdb=" N ASPAL 358 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGAP 163 " 0.342 9.50e-02 1.11e+02 1.53e-01 1.46e+01 pdb=" NE ARGAP 163 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARGAP 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARGAP 163 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARGAP 163 " 0.009 2.00e-02 2.50e+03 ... (remaining 6652 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 917 2.70 - 3.25: 35598 3.25 - 3.80: 56565 3.80 - 4.35: 77538 4.35 - 4.90: 129547 Nonbonded interactions: 300165 Sorted by model distance: nonbonded pdb=" O ILEAO 335 " pdb=" OG SERAO 340 " model vdw 2.144 3.040 nonbonded pdb=" O GLU i 52 " pdb=" CG GLU i 52 " model vdw 2.152 3.440 nonbonded pdb=" O LEU 9 179 " pdb=" ND2 ASN 9 182 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP g 84 " pdb=" OG SER i 73 " model vdw 2.232 3.040 nonbonded pdb=" O PRO c 86 " pdb=" NH1 ARG n 54 " model vdw 2.239 3.120 ... (remaining 300160 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 '0' selection = chain '9' } ncs_group { reference = (chain 'A' and (resid 2 through 51 or resid 65 through 262)) selection = (chain 'AP' and (resid 2 through 51 or resid 65 through 262)) selection = (chain 'AQ' and (resid 2 through 51 or resid 65 through 262)) selection = chain 'AR' selection = (chain 'B' and (resid 2 through 51 or resid 65 through 262)) selection = (chain 'C' and (resid 2 through 51 or resid 65 through 262)) } ncs_group { reference = chain 'AA' selection = chain 'AB' selection = (chain 'AC' and resid 338 through 356) selection = chain 'AD' selection = chain 'AE' } ncs_group { reference = (chain 'AF' and resid 334 through 354) selection = (chain 'AJ' and resid 334 through 354) selection = (chain 'AK' and resid 334 through 354) } ncs_group { reference = chain 'AG' selection = chain 'AH' selection = chain 'AI' } ncs_group { reference = chain 'AL' selection = (chain 'AM' and resid 330 through 361) selection = (chain 'AN' and resid 330 through 361) selection = chain 'AO' } ncs_group { reference = (chain 'b' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'c' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'd' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'e' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'f' and (resid 2 through 53 or resid 78 through 131)) } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.003 0.044 36655 Z= 0.174 Angle : 0.525 12.338 49667 Z= 0.316 Chirality : 0.040 0.225 5698 Planarity : 0.005 0.289 6655 Dihedral : 11.473 89.868 13607 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 2.97 % Allowed : 6.35 % Favored : 90.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.49 % 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: 0.22 (0.12), residues: 4708 helix: 1.09 (0.13), residues: 1467 sheet: -0.93 (0.18), residues: 762 loop : 0.05 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAP 163 TYR 0.011 0.001 TYR 9 116 PHE 0.026 0.001 PHE p 225 TRP 0.007 0.001 TRPAR 6 HIS 0.002 0.000 HIS o 184 Details of bonding type rmsd covalent geometry : bond 0.00289 (36655) covalent geometry : angle 0.52533 (49667) hydrogen bonds : bond 0.23084 ( 1597) hydrogen bonds : angle 6.90580 ( 4590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1147 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8075 (tttt) cc_final: 0.7673 (tppt) REVERT: 0 81 ASN cc_start: 0.8380 (m-40) cc_final: 0.8159 (m-40) REVERT: 0 118 ASN cc_start: 0.7331 (t0) cc_final: 0.7122 (t0) REVERT: 0 159 ILE cc_start: 0.7858 (pt) cc_final: 0.7588 (mt) REVERT: 0 174 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6370 (tptp) REVERT: 0 191 LEU cc_start: 0.5945 (tp) cc_final: 0.5553 (pp) REVERT: 9 28 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6588 (t80) REVERT: 9 81 ASN cc_start: 0.7803 (m-40) cc_final: 0.6631 (t0) REVERT: 9 85 LYS cc_start: 0.6411 (tttt) cc_final: 0.5609 (tmtt) REVERT: AB 349 ILE cc_start: 0.8968 (mt) cc_final: 0.8749 (mt) REVERT: AB 353 VAL cc_start: 0.8538 (t) cc_final: 0.8237 (t) REVERT: AC 342 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7804 (pt0) REVERT: AN 348 SER cc_start: 0.9124 (m) cc_final: 0.8696 (t) REVERT: AO 351 GLN cc_start: 0.8410 (tp40) cc_final: 0.8144 (tp-100) REVERT: B 30 SER cc_start: 0.8674 (m) cc_final: 0.8416 (p) REVERT: B 219 MET cc_start: 0.7984 (mtp) cc_final: 0.7710 (mtp) REVERT: C 111 ASN cc_start: 0.8352 (p0) cc_final: 0.8081 (m-40) REVERT: C 177 THR cc_start: 0.9136 (m) cc_final: 0.8577 (p) REVERT: C 179 PHE cc_start: 0.9002 (m-80) cc_final: 0.8661 (m-10) REVERT: C 259 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7903 (p0) REVERT: AP 236 GLU cc_start: 0.8196 (tt0) cc_final: 0.7895 (tt0) REVERT: AQ 100 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7473 (p0) REVERT: AR 77 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8634 (p) REVERT: AR 221 GLU cc_start: 0.5938 (tt0) cc_final: 0.5670 (tt0) REVERT: AR 242 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7671 (tp30) REVERT: AR 255 MET cc_start: 0.8008 (mtm) cc_final: 0.7593 (mmm) REVERT: c 106 ASN cc_start: 0.8845 (t0) cc_final: 0.8559 (t0) REVERT: d 47 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8545 (mmtm) REVERT: d 101 ASN cc_start: 0.8661 (t0) cc_final: 0.8355 (t0) REVERT: d 104 MET cc_start: 0.8862 (ttm) cc_final: 0.8651 (ttm) REVERT: e 93 THR cc_start: 0.8952 (p) cc_final: 0.8733 (t) REVERT: f 113 SER cc_start: 0.8566 (t) cc_final: 0.8255 (m) REVERT: h 67 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8548 (p) REVERT: h 84 ASP cc_start: 0.7817 (p0) cc_final: 0.7450 (p0) REVERT: h 105 MET cc_start: 0.8396 (mmm) cc_final: 0.8105 (mmt) REVERT: h 131 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7616 (mmp-170) REVERT: k 78 SER cc_start: 0.8915 (t) cc_final: 0.8602 (p) REVERT: l 43 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8710 (mttt) REVERT: m 44 MET cc_start: 0.8317 (ptp) cc_final: 0.7518 (ptp) REVERT: m 129 ILE cc_start: 0.8513 (mt) cc_final: 0.8110 (mt) REVERT: m 186 THR cc_start: 0.8691 (m) cc_final: 0.8419 (p) REVERT: n 60 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: n 115 ASN cc_start: 0.8512 (p0) cc_final: 0.8185 (p0) REVERT: n 158 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6299 (t80) REVERT: n 194 ASP cc_start: 0.8034 (t0) cc_final: 0.7826 (m-30) REVERT: n 239 ASP cc_start: 0.8206 (t70) cc_final: 0.7507 (t70) REVERT: o 55 VAL cc_start: 0.8140 (t) cc_final: 0.7932 (t) REVERT: o 158 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6822 (t80) REVERT: p 16 MET cc_start: 0.8374 (mmt) cc_final: 0.7843 (mmt) REVERT: p 162 ASP cc_start: 0.7143 (m-30) cc_final: 0.6891 (m-30) REVERT: q 97 GLU cc_start: 0.7933 (tt0) cc_final: 0.7568 (tt0) REVERT: q 200 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8130 (tm-30) REVERT: q 239 ASP cc_start: 0.7901 (t70) cc_final: 0.7510 (t0) REVERT: q 243 ASP cc_start: 0.8758 (t0) cc_final: 0.8531 (t70) outliers start: 118 outliers final: 24 residues processed: 1219 average time/residue: 0.2097 time to fit residues: 422.6981 Evaluate side-chains 830 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 796 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 174 LYS Chi-restraints excluded: chain 0 residue 176 ASN Chi-restraints excluded: chain 9 residue 28 PHE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain AL residue 339 LEU Chi-restraints excluded: chain AN residue 352 ASP Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AQ residue 100 ASP Chi-restraints excluded: chain AR residue 77 THR Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 4 SER Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 67 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 36 ASN 0 182 ASN 9 182 ASN A 15 GLN A 78 GLN A 111 ASN A 190 GLN A 191 ASN A 217 GLN A 226 ASN AA 351 GLN AC 341 ASN ** AJ 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 78 GLN B 217 GLN B 226 ASN C 15 GLN C 28 ASN C 51 GLN C 78 GLN C 166 GLN C 169 GLN C 173 GLN C 190 GLN C 226 ASN C 238 GLN AP 24 ASN AP 51 GLN AP 87 GLN AP 119 GLN AP 191 ASN AP 217 GLN AP 238 GLN AQ 24 ASN AQ 58 GLN AQ 87 GLN AQ 165 GLN AQ 203 GLN AQ 217 GLN AR 2 HIS AR 16 GLN AR 24 ASN AR 104 GLN AR 165 GLN AR 190 GLN AR 217 GLN AR 226 ASN AR 260 GLN b 105 GLN c 32 GLN c 106 ASN c 111 GLN d 105 GLN d 106 ASN d 107 GLN e 14 HIS e 34 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 ASN e 105 GLN e 107 GLN f 34 ASN f 105 GLN f 110 HIS g 100 ASN g 118 ASN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 GLN ** h 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 46 HIS i 100 ASN i 107 ASN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 46 HIS j 118 ASN k 22 ASN k 82 ASN k 100 ASN ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 100 ASN l 118 ASN m 24 ASN m 65 ASN m 179 ASN n 24 ASN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN p 119 HIS p 170 ASN p 179 ASN p 188 ASN p 222 GLN q 17 GLN q 20 GLN ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 222 GLN ** q 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134914 restraints weight = 52718.400| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.28 r_work: 0.3396 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36655 Z= 0.163 Angle : 0.566 10.528 49667 Z= 0.294 Chirality : 0.042 0.160 5698 Planarity : 0.004 0.048 6655 Dihedral : 5.024 59.790 5101 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 3.17 % Allowed : 12.45 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.00 (0.12), residues: 4708 helix: 2.60 (0.13), residues: 1463 sheet: -1.03 (0.18), residues: 704 loop : 0.08 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG k 131 TYR 0.017 0.002 TYR i 42 PHE 0.023 0.001 PHE c 121 TRP 0.013 0.001 TRP C 6 HIS 0.025 0.001 HIS n 184 Details of bonding type rmsd covalent geometry : bond 0.00366 (36655) covalent geometry : angle 0.56627 (49667) hydrogen bonds : bond 0.06231 ( 1597) hydrogen bonds : angle 4.41436 ( 4590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 848 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8213 (tttt) cc_final: 0.7496 (tppt) REVERT: 0 112 LYS cc_start: 0.7605 (mttt) cc_final: 0.7302 (tttm) REVERT: 0 120 THR cc_start: 0.7753 (m) cc_final: 0.7548 (m) REVERT: 0 191 LEU cc_start: 0.6446 (tp) cc_final: 0.6007 (pp) REVERT: 9 28 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7257 (t80) REVERT: 9 40 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8342 (ttm110) REVERT: 9 78 GLU cc_start: 0.8121 (tp30) cc_final: 0.7657 (tp30) REVERT: 9 85 LYS cc_start: 0.6336 (tttt) cc_final: 0.5275 (tmtt) REVERT: A 23 SER cc_start: 0.9326 (m) cc_final: 0.9028 (t) REVERT: A 67 MET cc_start: 0.9120 (mtp) cc_final: 0.8837 (mtt) REVERT: AB 353 VAL cc_start: 0.8799 (t) cc_final: 0.8499 (t) REVERT: AC 342 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7677 (pt0) REVERT: B 216 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.5311 (mmt90) REVERT: B 219 MET cc_start: 0.7021 (mtp) cc_final: 0.6436 (mtp) REVERT: C 140 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 177 THR cc_start: 0.9411 (m) cc_final: 0.8964 (p) REVERT: C 210 ASP cc_start: 0.6897 (t70) cc_final: 0.6233 (t70) REVERT: C 252 ASP cc_start: 0.8698 (t0) cc_final: 0.8479 (t0) REVERT: C 259 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8012 (p0) REVERT: C 261 GLN cc_start: 0.8471 (tp40) cc_final: 0.8174 (mm-40) REVERT: AP 55 GLN cc_start: 0.8610 (tp40) cc_final: 0.8333 (mm-40) REVERT: AR 157 GLU cc_start: 0.7557 (tp30) cc_final: 0.7305 (tp30) REVERT: AR 234 MET cc_start: 0.8391 (mmm) cc_final: 0.8178 (tpt) REVERT: b 87 ASP cc_start: 0.7484 (p0) cc_final: 0.7265 (p0) REVERT: c 106 ASN cc_start: 0.9120 (t0) cc_final: 0.8818 (t0) REVERT: d 47 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8420 (mmtm) REVERT: d 87 ASP cc_start: 0.8860 (p0) cc_final: 0.8544 (p0) REVERT: e 93 THR cc_start: 0.9117 (p) cc_final: 0.8814 (t) REVERT: g 10 THR cc_start: 0.8075 (p) cc_final: 0.7800 (p) REVERT: g 66 LYS cc_start: 0.8878 (ptmt) cc_final: 0.8584 (ptmt) REVERT: h 105 MET cc_start: 0.8782 (mmm) cc_final: 0.8543 (mmp) REVERT: h 131 ARG cc_start: 0.8711 (tpp80) cc_final: 0.7754 (mmp-170) REVERT: i 95 TYR cc_start: 0.8852 (m-80) cc_final: 0.8651 (m-80) REVERT: i 134 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7774 (mt0) REVERT: j 93 TYR cc_start: 0.9185 (m-80) cc_final: 0.8694 (m-80) REVERT: k 78 SER cc_start: 0.9055 (t) cc_final: 0.8713 (p) REVERT: k 91 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8126 (pt0) REVERT: k 126 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8700 (tttt) REVERT: l 43 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7828 (mtpp) REVERT: l 113 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8129 (mmm160) REVERT: l 117 THR cc_start: 0.8824 (t) cc_final: 0.8563 (m) REVERT: l 120 GLN cc_start: 0.8996 (mt0) cc_final: 0.8651 (mt0) REVERT: m 139 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7193 (mm-30) REVERT: m 194 ASP cc_start: 0.7879 (t0) cc_final: 0.7564 (t0) REVERT: m 220 ASP cc_start: 0.8987 (t70) cc_final: 0.8584 (t0) REVERT: n 158 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6045 (t80) REVERT: n 177 ASP cc_start: 0.9025 (t0) cc_final: 0.8772 (t70) REVERT: n 188 ASN cc_start: 0.8715 (m110) cc_final: 0.7768 (t0) REVERT: n 236 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8861 (tt0) REVERT: n 239 ASP cc_start: 0.8480 (t70) cc_final: 0.7832 (t70) REVERT: n 243 ASP cc_start: 0.8376 (t0) cc_final: 0.8044 (t0) REVERT: o 47 TYR cc_start: 0.8539 (m-80) cc_final: 0.8236 (m-80) REVERT: o 83 GLU cc_start: 0.5891 (tp30) cc_final: 0.5590 (mm-30) REVERT: o 158 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.6730 (t80) REVERT: o 165 LYS cc_start: 0.8639 (tttt) cc_final: 0.8397 (tttp) REVERT: o 231 MET cc_start: 0.8821 (tpp) cc_final: 0.8576 (tpt) REVERT: p 121 VAL cc_start: 0.9192 (t) cc_final: 0.8966 (p) REVERT: p 142 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7788 (tpp-160) REVERT: p 162 ASP cc_start: 0.7702 (m-30) cc_final: 0.7353 (m-30) REVERT: p 163 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8043 (ttt-90) REVERT: p 231 MET cc_start: 0.9034 (tpp) cc_final: 0.8691 (tpp) REVERT: q 9 MET cc_start: 0.8878 (tmm) cc_final: 0.8589 (ttp) REVERT: q 97 GLU cc_start: 0.8315 (tt0) cc_final: 0.8101 (tt0) REVERT: q 112 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: q 200 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8140 (tm-30) REVERT: q 243 ASP cc_start: 0.8823 (t0) cc_final: 0.8601 (t70) outliers start: 126 outliers final: 68 residues processed: 918 average time/residue: 0.1995 time to fit residues: 305.1405 Evaluate side-chains 816 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 739 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 176 ASN Chi-restraints excluded: chain 9 residue 28 PHE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain AB residue 348 SER Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AG residue 340 SER Chi-restraints excluded: chain AK residue 349 ILE Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 348 SER Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 236 GLU Chi-restraints excluded: chain AR residue 104 GLN Chi-restraints excluded: chain d residue 107 GLN Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 135 MET Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 112 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain l residue 34 VAL Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain l residue 124 SER Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 207 SER Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 112 MET Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 210 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 397 optimal weight: 10.0000 chunk 407 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 341 ASN AK 351 GLN AM 342 GLN AM 355 GLN AN 342 GLN AO 355 GLN C 173 GLN AP 190 GLN AP 238 GLN AQ 48 ASN AQ 50 ASN AR 261 GLN d 107 GLN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 ASN g 46 HIS g 85 HIS h 8 ASN h 22 ASN h 120 GLN i 107 ASN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN p 14 GLN p 24 ASN p 184 HIS p 222 GLN ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131587 restraints weight = 53027.160| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.27 r_work: 0.3364 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36655 Z= 0.157 Angle : 0.526 9.583 49667 Z= 0.269 Chirality : 0.042 0.148 5698 Planarity : 0.004 0.050 6655 Dihedral : 4.659 59.954 5074 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 3.75 % Allowed : 13.78 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.19 (0.12), residues: 4708 helix: 2.91 (0.13), residues: 1464 sheet: -1.19 (0.19), residues: 649 loop : 0.16 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG p 142 TYR 0.017 0.001 TYRAQ 241 PHE 0.014 0.001 PHE p 225 TRP 0.012 0.001 TRP A 6 HIS 0.004 0.001 HIS c 14 Details of bonding type rmsd covalent geometry : bond 0.00364 (36655) covalent geometry : angle 0.52616 (49667) hydrogen bonds : bond 0.05473 ( 1597) hydrogen bonds : angle 4.10780 ( 4590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 801 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8368 (tttt) cc_final: 0.7724 (tppt) REVERT: 0 89 SER cc_start: 0.7714 (p) cc_final: 0.7153 (m) REVERT: 0 159 ILE cc_start: 0.7492 (mt) cc_final: 0.7168 (tt) REVERT: 0 191 LEU cc_start: 0.6446 (tp) cc_final: 0.6077 (pp) REVERT: 9 28 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7453 (t80) REVERT: 9 40 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8212 (tp30) cc_final: 0.7747 (tp30) REVERT: 9 85 LYS cc_start: 0.6149 (tttt) cc_final: 0.5442 (tmtt) REVERT: 9 104 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 23 SER cc_start: 0.9329 (m) cc_final: 0.9016 (t) REVERT: A 61 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6535 (tm-30) REVERT: A 67 MET cc_start: 0.9126 (mtp) cc_final: 0.8812 (mtt) REVERT: AA 356 MET cc_start: 0.6061 (ptm) cc_final: 0.5858 (ptt) REVERT: AC 342 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7738 (pt0) REVERT: AK 352 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5154 (m-30) REVERT: B 216 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5439 (mmt90) REVERT: B 219 MET cc_start: 0.7398 (mtp) cc_final: 0.6743 (mtp) REVERT: C 140 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 177 THR cc_start: 0.9443 (m) cc_final: 0.9010 (p) REVERT: C 210 ASP cc_start: 0.7078 (t70) cc_final: 0.6428 (t70) REVERT: C 252 ASP cc_start: 0.8701 (t70) cc_final: 0.8489 (t0) REVERT: C 259 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8099 (p0) REVERT: C 261 GLN cc_start: 0.8418 (tp40) cc_final: 0.8159 (mm-40) REVERT: AP 55 GLN cc_start: 0.8413 (tp40) cc_final: 0.8078 (mm-40) REVERT: AP 262 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7022 (mp) REVERT: AQ 98 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6995 (mt-10) REVERT: AR 77 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8559 (p) REVERT: b 87 ASP cc_start: 0.7671 (p0) cc_final: 0.7388 (p0) REVERT: c 45 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: c 106 ASN cc_start: 0.9149 (t0) cc_final: 0.8877 (t0) REVERT: d 47 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8444 (mmtm) REVERT: e 13 GLN cc_start: 0.8635 (tt0) cc_final: 0.8286 (mt0) REVERT: f 20 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8042 (pt0) REVERT: g 10 THR cc_start: 0.7840 (p) cc_final: 0.7513 (p) REVERT: h 52 GLU cc_start: 0.8011 (mp0) cc_final: 0.7492 (mp0) REVERT: h 131 ARG cc_start: 0.8619 (tpp80) cc_final: 0.7793 (mmp-170) REVERT: h 134 GLN cc_start: 0.8166 (tp40) cc_final: 0.7884 (mm-40) REVERT: i 102 MET cc_start: 0.7772 (mmm) cc_final: 0.7118 (mpp) REVERT: i 134 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7835 (mt0) REVERT: j 32 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: j 93 TYR cc_start: 0.9171 (m-80) cc_final: 0.8492 (m-80) REVERT: k 52 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7573 (tm-30) REVERT: k 78 SER cc_start: 0.9042 (t) cc_final: 0.8761 (p) REVERT: k 82 ASN cc_start: 0.9066 (t0) cc_final: 0.8693 (m-40) REVERT: k 91 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8123 (pt0) REVERT: l 14 MET cc_start: 0.8880 (mtm) cc_final: 0.8481 (mtm) REVERT: l 66 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7912 (ptpp) REVERT: l 113 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8132 (mmp80) REVERT: l 120 GLN cc_start: 0.9100 (mt0) cc_final: 0.8857 (mt0) REVERT: m 194 ASP cc_start: 0.8229 (t0) cc_final: 0.7912 (t0) REVERT: m 220 ASP cc_start: 0.8906 (t70) cc_final: 0.8665 (t0) REVERT: n 16 MET cc_start: 0.8619 (mmt) cc_final: 0.8310 (tpt) REVERT: n 158 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.5938 (t80) REVERT: n 177 ASP cc_start: 0.9057 (t0) cc_final: 0.8759 (t70) REVERT: n 239 ASP cc_start: 0.8433 (t70) cc_final: 0.7766 (t70) REVERT: n 243 ASP cc_start: 0.8489 (t0) cc_final: 0.8230 (t70) REVERT: o 83 GLU cc_start: 0.6008 (tp30) cc_final: 0.5533 (mm-30) REVERT: o 158 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6958 (t80) REVERT: o 231 MET cc_start: 0.8995 (tpp) cc_final: 0.8753 (tpp) REVERT: p 16 MET cc_start: 0.8473 (mmt) cc_final: 0.8260 (mmt) REVERT: p 142 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7886 (tpp-160) REVERT: p 162 ASP cc_start: 0.7733 (m-30) cc_final: 0.7262 (m-30) REVERT: p 163 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.7991 (ttt-90) REVERT: p 231 MET cc_start: 0.9140 (tpp) cc_final: 0.8846 (tpp) REVERT: q 112 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: q 200 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8129 (tm-30) REVERT: q 205 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: q 237 GLU cc_start: 0.8909 (tp30) cc_final: 0.8708 (tp30) outliers start: 149 outliers final: 91 residues processed: 888 average time/residue: 0.1975 time to fit residues: 294.0749 Evaluate side-chains 818 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 713 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 176 ASN Chi-restraints excluded: chain 9 residue 28 PHE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AH residue 340 SER Chi-restraints excluded: chain AK residue 349 ILE Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 340 SER Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 17 THR Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AR residue 77 THR Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain d residue 107 GLN Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 112 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain j residue 32 ASP Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain l residue 34 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain l residue 124 SER Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 207 SER Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 194 ASP Chi-restraints excluded: chain o residue 204 ILE Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 242 SER Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 112 MET Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 60 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 74 optimal weight: 0.0270 chunk 152 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN AK 351 GLN AN 342 GLN B 59 ASN C 181 ASN b 29 ASN b 106 ASN ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 110 HIS ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN h 8 ASN i 116 GLN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 22 ASN ** l 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 102 ASN ** n 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN p 184 HIS ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129258 restraints weight = 53093.427| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.28 r_work: 0.3365 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36655 Z= 0.176 Angle : 0.543 11.593 49667 Z= 0.276 Chirality : 0.042 0.171 5698 Planarity : 0.004 0.052 6655 Dihedral : 4.539 59.790 5065 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 4.33 % Allowed : 14.39 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.15 (0.12), residues: 4708 helix: 2.92 (0.13), residues: 1462 sheet: -1.22 (0.18), residues: 704 loop : 0.14 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.017 0.002 TYR 9 116 PHE 0.015 0.001 PHE n 225 TRP 0.018 0.002 TRP C 6 HIS 0.004 0.001 HIS d 110 Details of bonding type rmsd covalent geometry : bond 0.00414 (36655) covalent geometry : angle 0.54275 (49667) hydrogen bonds : bond 0.05150 ( 1597) hydrogen bonds : angle 4.00676 ( 4590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 766 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8451 (tttt) cc_final: 0.7804 (tppt) REVERT: 0 159 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7171 (tt) REVERT: 9 28 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7626 (t80) REVERT: 9 40 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8003 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8290 (tp30) cc_final: 0.7786 (tp30) REVERT: 9 81 ASN cc_start: 0.7630 (m-40) cc_final: 0.6485 (t0) REVERT: 9 85 LYS cc_start: 0.6147 (tttt) cc_final: 0.5166 (tmtt) REVERT: A 23 SER cc_start: 0.9330 (m) cc_final: 0.9013 (t) REVERT: A 67 MET cc_start: 0.9114 (mtp) cc_final: 0.8787 (mtt) REVERT: A 112 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8474 (mp) REVERT: AC 342 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7568 (pt0) REVERT: AK 352 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.4983 (m-30) REVERT: AN 341 ASN cc_start: 0.8584 (m-40) cc_final: 0.8124 (m-40) REVERT: B 216 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5372 (mmt90) REVERT: B 219 MET cc_start: 0.7420 (mtp) cc_final: 0.6734 (mtp) REVERT: C 140 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7583 (mm-30) REVERT: C 177 THR cc_start: 0.9451 (m) cc_final: 0.8996 (p) REVERT: C 178 ASP cc_start: 0.8026 (t0) cc_final: 0.7789 (t0) REVERT: C 210 ASP cc_start: 0.7085 (t70) cc_final: 0.6477 (t70) REVERT: C 259 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8059 (p0) REVERT: C 261 GLN cc_start: 0.8524 (tp40) cc_final: 0.8235 (mm-40) REVERT: AP 55 GLN cc_start: 0.8375 (tp40) cc_final: 0.7932 (mm-40) REVERT: AP 98 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8542 (mp0) REVERT: AP 214 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7131 (mt-10) REVERT: AP 262 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.6833 (mp) REVERT: AR 157 GLU cc_start: 0.7485 (tp30) cc_final: 0.7239 (tp30) REVERT: b 87 ASP cc_start: 0.7817 (p0) cc_final: 0.7483 (p0) REVERT: c 45 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: c 106 ASN cc_start: 0.9263 (t0) cc_final: 0.8926 (t0) REVERT: d 47 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8318 (mmtm) REVERT: d 50 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7929 (tm-30) REVERT: d 111 GLN cc_start: 0.8864 (tp40) cc_final: 0.8035 (tp40) REVERT: e 13 GLN cc_start: 0.8769 (tt0) cc_final: 0.8337 (mt0) REVERT: e 88 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8378 (m) REVERT: f 20 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8069 (pt0) REVERT: g 10 THR cc_start: 0.7915 (p) cc_final: 0.7624 (p) REVERT: h 52 GLU cc_start: 0.8214 (mp0) cc_final: 0.7862 (mp0) REVERT: h 131 ARG cc_start: 0.8736 (tpp80) cc_final: 0.7893 (mmp-170) REVERT: i 134 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7965 (mt0) REVERT: j 14 MET cc_start: 0.8872 (mtm) cc_final: 0.8644 (mtp) REVERT: j 93 TYR cc_start: 0.9188 (m-80) cc_final: 0.8655 (m-80) REVERT: k 78 SER cc_start: 0.9044 (t) cc_final: 0.8770 (p) REVERT: k 91 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8141 (pt0) REVERT: l 113 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8114 (mmp80) REVERT: l 120 GLN cc_start: 0.9093 (mt0) cc_final: 0.8762 (mt0) REVERT: m 194 ASP cc_start: 0.8289 (t0) cc_final: 0.7934 (t0) REVERT: m 220 ASP cc_start: 0.8916 (t70) cc_final: 0.8671 (t0) REVERT: n 16 MET cc_start: 0.8660 (mmt) cc_final: 0.8379 (tpt) REVERT: n 60 GLU cc_start: 0.8444 (pt0) cc_final: 0.8181 (pt0) REVERT: n 158 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.5571 (t80) REVERT: n 239 ASP cc_start: 0.8473 (t70) cc_final: 0.7785 (t70) REVERT: n 243 ASP cc_start: 0.8530 (t0) cc_final: 0.8311 (t70) REVERT: o 158 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7100 (t80) REVERT: o 162 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: o 231 MET cc_start: 0.9004 (tpp) cc_final: 0.8761 (tpp) REVERT: p 1 MET cc_start: 0.8391 (pmm) cc_final: 0.8122 (ptp) REVERT: p 142 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8002 (tpp-160) REVERT: p 162 ASP cc_start: 0.7688 (m-30) cc_final: 0.7181 (m-30) REVERT: p 163 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: p 231 MET cc_start: 0.9148 (tpp) cc_final: 0.8911 (tpp) REVERT: q 16 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: q 83 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6273 (mm-30) REVERT: q 112 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: q 200 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8175 (tm-30) REVERT: q 237 GLU cc_start: 0.8908 (tp30) cc_final: 0.8654 (tp30) REVERT: q 238 MET cc_start: 0.9152 (mtm) cc_final: 0.8722 (mtp) outliers start: 172 outliers final: 112 residues processed: 870 average time/residue: 0.1938 time to fit residues: 283.6712 Evaluate side-chains 835 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 708 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 0 residue 176 ASN Chi-restraints excluded: chain 9 residue 28 PHE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AH residue 340 SER Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 340 SER Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 31 THR Chi-restraints excluded: chain AP residue 100 ASP Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 223 SER Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 17 THR Chi-restraints excluded: chain AQ residue 23 SER Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 131 SER Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 108 MET Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 112 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 32 ASP Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain l residue 34 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain l residue 124 SER Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 186 THR Chi-restraints excluded: chain m residue 207 SER Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 129 ILE Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain p residue 242 SER Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 112 MET Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 200 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 463 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 36 ASN 9 156 ASN AN 342 GLN b 29 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 120 GLN i 116 GLN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132097 restraints weight = 52451.279| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.25 r_work: 0.3421 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36655 Z= 0.108 Angle : 0.492 11.412 49667 Z= 0.249 Chirality : 0.040 0.184 5698 Planarity : 0.004 0.052 6655 Dihedral : 4.354 59.134 5065 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 3.33 % Allowed : 15.85 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.28 (0.12), residues: 4708 helix: 3.16 (0.13), residues: 1462 sheet: -1.21 (0.18), residues: 729 loop : 0.17 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 223 TYR 0.015 0.001 TYR d 80 PHE 0.022 0.001 PHE n 225 TRP 0.018 0.001 TRP C 6 HIS 0.003 0.000 HIS j 46 Details of bonding type rmsd covalent geometry : bond 0.00238 (36655) covalent geometry : angle 0.49155 (49667) hydrogen bonds : bond 0.04511 ( 1597) hydrogen bonds : angle 3.76798 ( 4590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 745 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8541 (tttt) cc_final: 0.7879 (tppt) REVERT: 0 98 ASN cc_start: 0.7566 (t0) cc_final: 0.7327 (m-40) REVERT: 0 159 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7188 (tt) REVERT: 9 28 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7773 (t80) REVERT: 9 40 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8223 (tp30) cc_final: 0.7696 (tp30) REVERT: 9 85 LYS cc_start: 0.6214 (tttt) cc_final: 0.5129 (tmtt) REVERT: 9 116 TYR cc_start: 0.8360 (p90) cc_final: 0.8135 (p90) REVERT: 9 151 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7457 (mt) REVERT: A 23 SER cc_start: 0.9278 (m) cc_final: 0.8964 (t) REVERT: A 112 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (mp) REVERT: AA 352 ASP cc_start: 0.8282 (t0) cc_final: 0.7964 (t0) REVERT: AB 356 MET cc_start: 0.7908 (tpt) cc_final: 0.7681 (mmm) REVERT: AC 342 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7403 (pt0) REVERT: AI 342 GLN cc_start: 0.9021 (tt0) cc_final: 0.8289 (mm110) REVERT: AK 352 ASP cc_start: 0.5545 (OUTLIER) cc_final: 0.4986 (m-30) REVERT: AL 341 ASN cc_start: 0.8804 (m-40) cc_final: 0.8563 (m110) REVERT: AN 341 ASN cc_start: 0.8497 (m-40) cc_final: 0.8111 (m-40) REVERT: B 216 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5839 (mmt90) REVERT: B 219 MET cc_start: 0.7486 (mtp) cc_final: 0.6788 (mtp) REVERT: C 140 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 177 THR cc_start: 0.9387 (m) cc_final: 0.8994 (p) REVERT: C 185 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9050 (mt) REVERT: C 210 ASP cc_start: 0.7123 (t70) cc_final: 0.6535 (t70) REVERT: C 259 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8233 (p0) REVERT: C 261 GLN cc_start: 0.8503 (tp40) cc_final: 0.8234 (mm-40) REVERT: AP 55 GLN cc_start: 0.8360 (tp40) cc_final: 0.7925 (mm-40) REVERT: AP 125 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8440 (mp0) REVERT: AP 236 GLU cc_start: 0.8413 (tt0) cc_final: 0.7865 (tt0) REVERT: AP 262 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6747 (mp) REVERT: AQ 209 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7440 (pp) REVERT: AR 234 MET cc_start: 0.8007 (tpt) cc_final: 0.7696 (tpt) REVERT: c 45 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: c 106 ASN cc_start: 0.9242 (t0) cc_final: 0.9011 (t0) REVERT: d 47 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8163 (mmtm) REVERT: d 50 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7868 (tm-30) REVERT: d 111 GLN cc_start: 0.8878 (tp40) cc_final: 0.8028 (tp40) REVERT: e 13 GLN cc_start: 0.8732 (tt0) cc_final: 0.8298 (mt0) REVERT: f 20 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8004 (pt0) REVERT: h 52 GLU cc_start: 0.8202 (mp0) cc_final: 0.7822 (mp0) REVERT: h 84 ASP cc_start: 0.8111 (p0) cc_final: 0.7834 (p0) REVERT: h 96 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8793 (mttm) REVERT: h 131 ARG cc_start: 0.8695 (tpp80) cc_final: 0.8107 (mmp-170) REVERT: h 134 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7808 (mp10) REVERT: i 93 TYR cc_start: 0.8666 (m-10) cc_final: 0.8228 (m-10) REVERT: i 134 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7966 (mt0) REVERT: i 135 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.4497 (ttp) REVERT: j 32 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: j 80 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8255 (mt-10) REVERT: j 93 TYR cc_start: 0.9158 (m-80) cc_final: 0.8346 (m-80) REVERT: k 78 SER cc_start: 0.8990 (t) cc_final: 0.8691 (p) REVERT: k 91 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8065 (pt0) REVERT: l 113 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7441 (mmp-170) REVERT: m 194 ASP cc_start: 0.8238 (t0) cc_final: 0.7868 (t0) REVERT: n 16 MET cc_start: 0.8602 (mmt) cc_final: 0.8294 (tpt) REVERT: n 158 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.5586 (t80) REVERT: n 239 ASP cc_start: 0.8409 (t70) cc_final: 0.7701 (t70) REVERT: o 158 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.6985 (t80) REVERT: o 231 MET cc_start: 0.9018 (tpp) cc_final: 0.8734 (tpp) REVERT: p 1 MET cc_start: 0.8403 (pmm) cc_final: 0.8163 (ptp) REVERT: p 7 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8875 (mt) REVERT: p 121 VAL cc_start: 0.9076 (t) cc_final: 0.8839 (p) REVERT: p 142 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7997 (tpp-160) REVERT: p 162 ASP cc_start: 0.7583 (m-30) cc_final: 0.7064 (m-30) REVERT: p 163 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8218 (ttm-80) REVERT: q 16 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: q 65 ASN cc_start: 0.8804 (t0) cc_final: 0.8569 (t0) REVERT: q 200 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8173 (tm-30) REVERT: q 205 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: q 237 GLU cc_start: 0.8871 (tp30) cc_final: 0.8585 (tp30) REVERT: q 238 MET cc_start: 0.9075 (mtm) cc_final: 0.8578 (mtp) outliers start: 132 outliers final: 79 residues processed: 819 average time/residue: 0.1972 time to fit residues: 271.0856 Evaluate side-chains 800 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 702 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 0 residue 176 ASN Chi-restraints excluded: chain 9 residue 28 PHE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain AG residue 340 SER Chi-restraints excluded: chain AI residue 335 ILE Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 355 GLN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain AN residue 358 ASP Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 100 ASP Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 125 GLU Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 32 ASP Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain l residue 124 SER Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 22 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 459 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 326 optimal weight: 0.6980 chunk 387 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 156 ASN AM 355 GLN AN 342 GLN AO 341 ASN AO 355 GLN AP 104 GLN AQ 48 ASN AR 48 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 ASN h 120 GLN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN p 188 ASN q 125 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128058 restraints weight = 53286.489| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.26 r_work: 0.3362 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36655 Z= 0.186 Angle : 0.555 10.049 49667 Z= 0.281 Chirality : 0.043 0.194 5698 Planarity : 0.004 0.057 6655 Dihedral : 4.475 59.767 5062 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 4.46 % Allowed : 15.42 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.14 (0.12), residues: 4708 helix: 3.00 (0.13), residues: 1462 sheet: -1.28 (0.17), residues: 765 loop : 0.14 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAP 216 TYR 0.016 0.001 TYRAQ 241 PHE 0.015 0.001 PHE n 225 TRP 0.018 0.002 TRP C 6 HIS 0.005 0.001 HISAP 2 Details of bonding type rmsd covalent geometry : bond 0.00441 (36655) covalent geometry : angle 0.55537 (49667) hydrogen bonds : bond 0.04886 ( 1597) hydrogen bonds : angle 3.91272 ( 4590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 746 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8630 (tttt) cc_final: 0.7880 (tppt) REVERT: 0 159 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7275 (tt) REVERT: 9 40 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8088 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8301 (tp30) cc_final: 0.7785 (tp30) REVERT: 9 85 LYS cc_start: 0.6018 (tttt) cc_final: 0.5019 (tmtt) REVERT: 9 117 LEU cc_start: 0.8557 (tp) cc_final: 0.8286 (tp) REVERT: 9 151 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 23 SER cc_start: 0.9301 (m) cc_final: 0.8996 (t) REVERT: A 67 MET cc_start: 0.9007 (mtt) cc_final: 0.8784 (mtt) REVERT: A 112 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8618 (mp) REVERT: AA 352 ASP cc_start: 0.8316 (t0) cc_final: 0.8024 (t0) REVERT: AB 356 MET cc_start: 0.8361 (tpt) cc_final: 0.7946 (mmm) REVERT: AC 342 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7566 (pt0) REVERT: AK 352 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5045 (m-30) REVERT: AN 341 ASN cc_start: 0.8596 (m-40) cc_final: 0.8172 (m-40) REVERT: B 216 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.5968 (mmt90) REVERT: B 219 MET cc_start: 0.7396 (mtp) cc_final: 0.7185 (mtp) REVERT: C 185 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9079 (mt) REVERT: AP 55 GLN cc_start: 0.8321 (tp40) cc_final: 0.7920 (tp40) REVERT: AP 214 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7150 (mt-10) REVERT: AP 262 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6835 (mp) REVERT: AQ 209 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7503 (pp) REVERT: AQ 216 ARG cc_start: 0.8519 (mmt180) cc_final: 0.8272 (mmt-90) REVERT: AR 214 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6432 (mt-10) REVERT: c 45 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: c 106 ASN cc_start: 0.9346 (t0) cc_final: 0.8962 (t0) REVERT: d 41 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.7938 (mmm-85) REVERT: d 47 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8168 (mmtm) REVERT: d 50 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7883 (tm-30) REVERT: d 111 GLN cc_start: 0.8998 (tp40) cc_final: 0.8185 (tp40) REVERT: f 20 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8029 (pt0) REVERT: g 10 THR cc_start: 0.8041 (p) cc_final: 0.7767 (p) REVERT: h 30 ASN cc_start: 0.8306 (m-40) cc_final: 0.8098 (t0) REVERT: h 52 GLU cc_start: 0.8266 (mp0) cc_final: 0.7907 (mp0) REVERT: h 84 ASP cc_start: 0.8135 (p0) cc_final: 0.7787 (p0) REVERT: h 96 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8765 (mttm) REVERT: h 127 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7856 (mm-40) REVERT: h 131 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8016 (mmp-170) REVERT: i 135 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4848 (ttp) REVERT: j 80 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8153 (mt-10) REVERT: k 52 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7741 (tm-30) REVERT: k 91 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8092 (pt0) REVERT: l 113 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7503 (mmp-170) REVERT: m 161 VAL cc_start: 0.8174 (m) cc_final: 0.7942 (p) REVERT: m 194 ASP cc_start: 0.8481 (t0) cc_final: 0.8066 (t0) REVERT: n 16 MET cc_start: 0.8672 (mmt) cc_final: 0.8358 (tpt) REVERT: n 158 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.5580 (t80) REVERT: o 158 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7191 (t80) REVERT: o 162 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: o 231 MET cc_start: 0.9019 (tpp) cc_final: 0.8684 (tpt) REVERT: p 1 MET cc_start: 0.8440 (pmm) cc_final: 0.8131 (ptp) REVERT: p 142 ARG cc_start: 0.8421 (tpp80) cc_final: 0.7987 (tpp-160) REVERT: p 162 ASP cc_start: 0.7644 (m-30) cc_final: 0.7149 (m-30) REVERT: p 163 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: q 16 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8048 (tpp) REVERT: q 65 ASN cc_start: 0.8790 (t0) cc_final: 0.8556 (t0) REVERT: q 200 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8126 (tm-30) REVERT: q 237 GLU cc_start: 0.8913 (tp30) cc_final: 0.8593 (tp30) REVERT: q 238 MET cc_start: 0.9023 (mtm) cc_final: 0.8447 (mtp) outliers start: 177 outliers final: 114 residues processed: 850 average time/residue: 0.2003 time to fit residues: 285.1035 Evaluate side-chains 849 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 720 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 28 PHE Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 151 LEU Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain AC residue 349 ILE Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 330 ASN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain AP residue 31 THR Chi-restraints excluded: chain AP residue 100 ASP Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 223 SER Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 23 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 125 GLU Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 96 MET Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain h residue 22 ASN Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 84 ASP Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 186 THR Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 129 ILE Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 227 MET Chi-restraints excluded: chain q residue 241 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 399 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 327 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AN 342 GLN AO 341 ASN AP 81 HIS AQ 191 ASN b 29 ASN b 101 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 120 GLN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 HIS k 82 ASN ** l 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 159 GLN o 228 GLN q 125 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127166 restraints weight = 52618.963| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3329 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36655 Z= 0.200 Angle : 0.565 9.980 49667 Z= 0.288 Chirality : 0.043 0.194 5698 Planarity : 0.004 0.056 6655 Dihedral : 4.423 59.850 5053 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 4.31 % Allowed : 16.15 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.04 (0.12), residues: 4708 helix: 2.92 (0.13), residues: 1463 sheet: -1.33 (0.17), residues: 765 loop : 0.06 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG q 163 TYR 0.019 0.002 TYR 9 116 PHE 0.018 0.001 PHE n 225 TRP 0.019 0.002 TRP C 6 HIS 0.004 0.001 HIS q 184 Details of bonding type rmsd covalent geometry : bond 0.00475 (36655) covalent geometry : angle 0.56462 (49667) hydrogen bonds : bond 0.04993 ( 1597) hydrogen bonds : angle 3.97244 ( 4590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 743 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8629 (tttt) cc_final: 0.7830 (tppt) REVERT: 0 159 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7346 (tt) REVERT: 9 40 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8294 (tp30) cc_final: 0.7780 (tp30) REVERT: 9 85 LYS cc_start: 0.6179 (tttt) cc_final: 0.5044 (tmtt) REVERT: 9 117 LEU cc_start: 0.8566 (tp) cc_final: 0.8321 (tp) REVERT: A 249 SER cc_start: 0.9379 (t) cc_final: 0.9172 (t) REVERT: AA 352 ASP cc_start: 0.8320 (t0) cc_final: 0.8050 (t0) REVERT: AC 342 GLN cc_start: 0.8631 (mm-40) cc_final: 0.7529 (pt0) REVERT: AK 352 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5130 (m-30) REVERT: AN 341 ASN cc_start: 0.8606 (m-40) cc_final: 0.8222 (m-40) REVERT: AN 357 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8045 (ttmm) REVERT: B 219 MET cc_start: 0.7413 (mtp) cc_final: 0.6792 (mtp) REVERT: C 128 LEU cc_start: 0.7994 (tp) cc_final: 0.7779 (tt) REVERT: C 177 THR cc_start: 0.9459 (m) cc_final: 0.9086 (p) REVERT: C 185 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9041 (mt) REVERT: C 261 GLN cc_start: 0.8535 (tp40) cc_final: 0.8165 (mm-40) REVERT: AP 55 GLN cc_start: 0.8243 (tp40) cc_final: 0.7928 (tp40) REVERT: AP 98 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: AP 262 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6731 (mp) REVERT: AQ 209 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7571 (pp) REVERT: AQ 216 ARG cc_start: 0.8464 (mmt180) cc_final: 0.7937 (mmt-90) REVERT: c 45 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: c 106 ASN cc_start: 0.9377 (t0) cc_final: 0.8977 (t0) REVERT: d 41 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: d 47 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8104 (mmtm) REVERT: d 50 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7864 (tm-30) REVERT: d 111 GLN cc_start: 0.9041 (tp40) cc_final: 0.8275 (tp40) REVERT: e 13 GLN cc_start: 0.8738 (tt0) cc_final: 0.8373 (mt0) REVERT: f 20 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8010 (pt0) REVERT: g 10 THR cc_start: 0.8166 (p) cc_final: 0.7927 (p) REVERT: h 52 GLU cc_start: 0.8376 (mp0) cc_final: 0.7927 (mp0) REVERT: h 84 ASP cc_start: 0.8061 (p0) cc_final: 0.7760 (p0) REVERT: h 96 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8762 (mttm) REVERT: h 120 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8541 (mm-40) REVERT: h 127 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7917 (mm-40) REVERT: h 131 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8058 (mmp-170) REVERT: j 80 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8195 (mt-10) REVERT: k 52 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7702 (tm-30) REVERT: k 91 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8094 (pt0) REVERT: l 113 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7571 (mmp-170) REVERT: m 194 ASP cc_start: 0.8534 (t0) cc_final: 0.8079 (t0) REVERT: n 16 MET cc_start: 0.8660 (mmt) cc_final: 0.8329 (tpt) REVERT: n 158 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.5769 (t80) REVERT: n 248 MET cc_start: 0.8007 (mtm) cc_final: 0.7795 (mtt) REVERT: o 158 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7221 (t80) REVERT: o 162 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: o 228 GLN cc_start: 0.8641 (mt0) cc_final: 0.8096 (mt0) REVERT: o 231 MET cc_start: 0.9007 (tpp) cc_final: 0.8685 (tpt) REVERT: p 1 MET cc_start: 0.8462 (pmm) cc_final: 0.8093 (ptp) REVERT: p 142 ARG cc_start: 0.8392 (tpp80) cc_final: 0.7979 (tpp-160) REVERT: p 162 ASP cc_start: 0.7684 (m-30) cc_final: 0.7200 (m-30) REVERT: p 243 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8219 (t0) REVERT: q 16 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7865 (tpp) REVERT: q 65 ASN cc_start: 0.8827 (t0) cc_final: 0.8581 (t0) REVERT: q 112 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7758 (ttm) REVERT: q 200 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8198 (tm-30) REVERT: q 205 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: q 238 MET cc_start: 0.9127 (mtm) cc_final: 0.8601 (mtp) outliers start: 171 outliers final: 118 residues processed: 847 average time/residue: 0.1938 time to fit residues: 277.2105 Evaluate side-chains 849 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 715 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 28 PHE Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain AC residue 349 ILE Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AG residue 340 SER Chi-restraints excluded: chain AH residue 340 SER Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 349 ILE Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 330 ASN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain AP residue 31 THR Chi-restraints excluded: chain AP residue 98 GLU Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 23 SER Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 93 LEU Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 125 GLU Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 96 MET Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain d residue 104 MET Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 108 MET Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 120 GLN Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 186 THR Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 120 LEU Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 129 ILE Chi-restraints excluded: chain p residue 130 THR Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 112 MET Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Chi-restraints excluded: chain q residue 227 MET Chi-restraints excluded: chain q residue 241 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 170 optimal weight: 0.3980 chunk 146 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 456 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AM 342 GLN AN 342 GLN AP 59 ASN ** AQ 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 ASN b 101 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 22 ASN h 120 GLN ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** l 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 ASN ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127771 restraints weight = 52754.604| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.24 r_work: 0.3351 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36655 Z= 0.136 Angle : 0.531 10.089 49667 Z= 0.268 Chirality : 0.041 0.203 5698 Planarity : 0.004 0.055 6655 Dihedral : 4.304 59.860 5053 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 3.83 % Allowed : 17.16 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.17 (0.12), residues: 4708 helix: 3.07 (0.13), residues: 1464 sheet: -1.24 (0.18), residues: 715 loop : 0.08 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG k 131 TYR 0.020 0.001 TYR 9 116 PHE 0.018 0.001 PHE n 225 TRP 0.016 0.001 TRP A 6 HIS 0.004 0.001 HIS j 46 Details of bonding type rmsd covalent geometry : bond 0.00318 (36655) covalent geometry : angle 0.53077 (49667) hydrogen bonds : bond 0.04633 ( 1597) hydrogen bonds : angle 3.83415 ( 4590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 745 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8543 (tttt) cc_final: 0.7733 (tppt) REVERT: 0 159 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7316 (tt) REVERT: 9 21 GLU cc_start: 0.7415 (tt0) cc_final: 0.7190 (tt0) REVERT: 9 40 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8298 (tp30) cc_final: 0.7757 (tp30) REVERT: 9 85 LYS cc_start: 0.6179 (tttt) cc_final: 0.5023 (tmtt) REVERT: 9 117 LEU cc_start: 0.8630 (tp) cc_final: 0.8419 (tp) REVERT: 9 151 LEU cc_start: 0.7775 (tt) cc_final: 0.7490 (mt) REVERT: A 23 SER cc_start: 0.9392 (m) cc_final: 0.8923 (t) REVERT: AA 352 ASP cc_start: 0.8330 (t0) cc_final: 0.8028 (t0) REVERT: AC 342 GLN cc_start: 0.8621 (mm-40) cc_final: 0.7519 (pt0) REVERT: AE 356 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7847 (mtm) REVERT: AF 351 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7699 (tp-100) REVERT: AK 352 ASP cc_start: 0.5631 (OUTLIER) cc_final: 0.5125 (m-30) REVERT: AM 330 ASN cc_start: 0.7142 (t0) cc_final: 0.6389 (t0) REVERT: AN 341 ASN cc_start: 0.8575 (m-40) cc_final: 0.8210 (m-40) REVERT: AN 357 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8008 (ttmm) REVERT: AO 331 MET cc_start: 0.8808 (mmm) cc_final: 0.8309 (ttm) REVERT: B 216 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.5966 (mmt90) REVERT: B 219 MET cc_start: 0.7436 (mtp) cc_final: 0.7189 (mtp) REVERT: C 138 GLU cc_start: 0.8840 (tp30) cc_final: 0.8574 (tp30) REVERT: C 140 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7484 (mm-30) REVERT: C 177 THR cc_start: 0.9441 (m) cc_final: 0.9071 (p) REVERT: C 185 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9035 (mt) REVERT: C 221 GLU cc_start: 0.8557 (tt0) cc_final: 0.8333 (tt0) REVERT: C 259 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8428 (p0) REVERT: C 261 GLN cc_start: 0.8468 (tp40) cc_final: 0.8148 (mm-40) REVERT: AP 55 GLN cc_start: 0.8247 (tp40) cc_final: 0.7945 (tp40) REVERT: AP 125 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8513 (mp0) REVERT: AP 262 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6755 (mp) REVERT: AQ 209 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7600 (pp) REVERT: AR 250 SER cc_start: 0.8866 (m) cc_final: 0.8563 (t) REVERT: c 45 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: c 106 ASN cc_start: 0.9355 (t0) cc_final: 0.8958 (t0) REVERT: d 41 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: d 47 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8242 (mmtm) REVERT: d 111 GLN cc_start: 0.9023 (tp40) cc_final: 0.8023 (tp40) REVERT: e 13 GLN cc_start: 0.8714 (tt0) cc_final: 0.8345 (mt0) REVERT: f 20 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7984 (pt0) REVERT: g 10 THR cc_start: 0.8092 (p) cc_final: 0.7858 (p) REVERT: h 8 ASN cc_start: 0.7965 (m110) cc_final: 0.7758 (m-40) REVERT: h 52 GLU cc_start: 0.8316 (mp0) cc_final: 0.7982 (mp0) REVERT: h 84 ASP cc_start: 0.8021 (p0) cc_final: 0.7740 (p0) REVERT: h 96 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8736 (mttm) REVERT: h 131 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8071 (mmp-170) REVERT: i 135 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.4949 (ttp) REVERT: j 80 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8173 (mt-10) REVERT: k 52 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7610 (tm-30) REVERT: k 82 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8426 (m110) REVERT: k 91 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8093 (pt0) REVERT: l 39 LYS cc_start: 0.8412 (tptt) cc_final: 0.8133 (tppt) REVERT: l 110 SER cc_start: 0.9176 (t) cc_final: 0.8966 (p) REVERT: l 113 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7506 (mmp-170) REVERT: m 109 GLN cc_start: 0.8271 (pm20) cc_final: 0.8055 (pm20) REVERT: m 112 MET cc_start: 0.7959 (mtm) cc_final: 0.7732 (mtp) REVERT: m 194 ASP cc_start: 0.8515 (t0) cc_final: 0.8049 (t0) REVERT: n 16 MET cc_start: 0.8631 (mmt) cc_final: 0.8269 (tpt) REVERT: n 158 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.5830 (t80) REVERT: n 188 ASN cc_start: 0.8694 (m110) cc_final: 0.7770 (t0) REVERT: n 218 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8279 (mp) REVERT: o 158 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7131 (t80) REVERT: o 162 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: o 228 GLN cc_start: 0.8624 (mt0) cc_final: 0.8302 (mt0) REVERT: o 231 MET cc_start: 0.9017 (tpp) cc_final: 0.8683 (tpt) REVERT: p 1 MET cc_start: 0.8431 (pmm) cc_final: 0.8090 (ptp) REVERT: p 142 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7979 (tpp-160) REVERT: p 162 ASP cc_start: 0.7620 (m-30) cc_final: 0.7127 (m-30) REVERT: q 16 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7833 (tpp) REVERT: q 65 ASN cc_start: 0.8772 (t0) cc_final: 0.8557 (t0) REVERT: q 200 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8127 (tm-30) REVERT: q 205 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: q 238 MET cc_start: 0.8952 (mtm) cc_final: 0.8450 (mtp) outliers start: 152 outliers final: 110 residues processed: 833 average time/residue: 0.2052 time to fit residues: 288.3309 Evaluate side-chains 851 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 723 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 49 SER Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain AC residue 349 ILE Chi-restraints excluded: chain AE residue 356 MET Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AG residue 340 SER Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 349 ILE Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 330 ASN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 358 ASP Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 125 GLU Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 96 MET Chi-restraints excluded: chain AR residue 104 GLN Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 108 MET Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 32 ASP Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 186 THR Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 218 LEU Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 240 LYS Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 129 ILE Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Chi-restraints excluded: chain q residue 241 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 367 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 395 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 401 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 403 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AJ 355 GLN AM 342 GLN AN 342 GLN ** AQ 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN q 125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127547 restraints weight = 52913.428| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.23 r_work: 0.3372 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36655 Z= 0.151 Angle : 0.545 13.571 49667 Z= 0.275 Chirality : 0.042 0.206 5698 Planarity : 0.004 0.055 6655 Dihedral : 4.307 59.843 5053 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 3.78 % Allowed : 17.38 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.17 (0.12), residues: 4708 helix: 3.03 (0.13), residues: 1464 sheet: -1.23 (0.18), residues: 727 loop : 0.11 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 163 TYR 0.019 0.001 TYR i 42 PHE 0.018 0.001 PHE n 225 TRP 0.017 0.001 TRP C 6 HIS 0.004 0.001 HISAP 2 Details of bonding type rmsd covalent geometry : bond 0.00355 (36655) covalent geometry : angle 0.54485 (49667) hydrogen bonds : bond 0.04594 ( 1597) hydrogen bonds : angle 3.83128 ( 4590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 723 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8558 (tttt) cc_final: 0.7752 (tppt) REVERT: 0 159 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7335 (tt) REVERT: 9 21 GLU cc_start: 0.7372 (tt0) cc_final: 0.7151 (tt0) REVERT: 9 40 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8258 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8254 (tp30) cc_final: 0.7704 (tp30) REVERT: 9 85 LYS cc_start: 0.6188 (tttt) cc_final: 0.5027 (tmtt) REVERT: 9 117 LEU cc_start: 0.8613 (tp) cc_final: 0.8389 (tp) REVERT: 9 151 LEU cc_start: 0.7939 (tt) cc_final: 0.7574 (mt) REVERT: A 23 SER cc_start: 0.9394 (m) cc_final: 0.8925 (t) REVERT: AA 352 ASP cc_start: 0.8310 (t0) cc_final: 0.8023 (t0) REVERT: AC 342 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7526 (pt0) REVERT: AE 356 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: AF 351 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7725 (tp-100) REVERT: AK 352 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5112 (m-30) REVERT: AM 330 ASN cc_start: 0.7135 (t0) cc_final: 0.6496 (t0) REVERT: AN 341 ASN cc_start: 0.8579 (m-40) cc_final: 0.8181 (m-40) REVERT: AN 357 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8014 (ttmm) REVERT: B 216 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5949 (mmt90) REVERT: B 219 MET cc_start: 0.7409 (mtp) cc_final: 0.7171 (mtp) REVERT: C 1 MET cc_start: 0.7518 (pmm) cc_final: 0.7233 (pmm) REVERT: C 140 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 177 THR cc_start: 0.9448 (m) cc_final: 0.9062 (p) REVERT: C 185 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9051 (mt) REVERT: C 259 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8429 (p0) REVERT: C 261 GLN cc_start: 0.8459 (tp40) cc_final: 0.8141 (mm-40) REVERT: AP 55 GLN cc_start: 0.8230 (tp40) cc_final: 0.7955 (tp40) REVERT: AP 125 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8498 (mp0) REVERT: AP 262 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6756 (mp) REVERT: AQ 209 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7583 (pp) REVERT: c 45 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: c 106 ASN cc_start: 0.9349 (t0) cc_final: 0.8928 (t0) REVERT: d 41 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: d 47 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8236 (mmtm) REVERT: d 111 GLN cc_start: 0.8991 (tp40) cc_final: 0.8258 (tp40) REVERT: e 13 GLN cc_start: 0.8705 (tt0) cc_final: 0.8333 (mt0) REVERT: f 20 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7989 (pt0) REVERT: g 10 THR cc_start: 0.8019 (p) cc_final: 0.7766 (p) REVERT: g 105 MET cc_start: 0.8655 (mmm) cc_final: 0.8372 (mmm) REVERT: h 52 GLU cc_start: 0.8291 (mp0) cc_final: 0.7978 (mp0) REVERT: h 84 ASP cc_start: 0.8006 (p0) cc_final: 0.7734 (p0) REVERT: h 96 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8678 (mttm) REVERT: h 131 ARG cc_start: 0.8783 (tpp80) cc_final: 0.8081 (mmp-170) REVERT: i 135 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.5014 (ttp) REVERT: j 52 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7898 (tm-30) REVERT: j 80 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8208 (mt-10) REVERT: k 52 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7646 (tm-30) REVERT: k 91 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8076 (pt0) REVERT: l 39 LYS cc_start: 0.8442 (tptt) cc_final: 0.8176 (tppt) REVERT: l 110 SER cc_start: 0.9180 (t) cc_final: 0.8961 (p) REVERT: l 113 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8050 (mmp80) REVERT: m 112 MET cc_start: 0.7977 (mtm) cc_final: 0.7752 (mtp) REVERT: m 194 ASP cc_start: 0.8555 (t0) cc_final: 0.8078 (t0) REVERT: n 16 MET cc_start: 0.8638 (mmt) cc_final: 0.8257 (tpt) REVERT: n 158 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.5835 (t80) REVERT: n 188 ASN cc_start: 0.8704 (m110) cc_final: 0.7799 (t0) REVERT: n 218 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (mp) REVERT: o 158 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7114 (t80) REVERT: o 162 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: o 228 GLN cc_start: 0.8635 (mt0) cc_final: 0.8306 (mt0) REVERT: o 231 MET cc_start: 0.9086 (tpp) cc_final: 0.8833 (tpt) REVERT: p 1 MET cc_start: 0.8456 (pmm) cc_final: 0.8166 (ptp) REVERT: p 58 MET cc_start: 0.8532 (mtp) cc_final: 0.8293 (mtm) REVERT: p 142 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7995 (tpp-160) REVERT: p 162 ASP cc_start: 0.7604 (m-30) cc_final: 0.7108 (m-30) REVERT: p 163 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7929 (ttt-90) REVERT: q 16 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7977 (tpp) REVERT: q 65 ASN cc_start: 0.8773 (t0) cc_final: 0.8550 (t0) REVERT: q 200 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8111 (tm-30) REVERT: q 205 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: q 238 MET cc_start: 0.8963 (mtm) cc_final: 0.8469 (mtp) outliers start: 150 outliers final: 118 residues processed: 809 average time/residue: 0.2027 time to fit residues: 274.7665 Evaluate side-chains 849 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 714 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 151 LEU Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain AB residue 341 ASN Chi-restraints excluded: chain AC residue 349 ILE Chi-restraints excluded: chain AE residue 356 MET Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AG residue 340 SER Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 349 ILE Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 330 ASN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 358 ASP Chi-restraints excluded: chain AN residue 348 SER Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 31 THR Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 96 MET Chi-restraints excluded: chain AR residue 104 GLN Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 45 PHE Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 108 MET Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain g residue 135 MET Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 108 MET Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 32 ASP Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 186 THR Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 120 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain n residue 218 LEU Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 240 LYS Chi-restraints excluded: chain o residue 244 SER Chi-restraints excluded: chain p residue 130 THR Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 240 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Chi-restraints excluded: chain q residue 241 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 68 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 441 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 414 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AJ 355 GLN AN 342 GLN AO 341 ASN AO 355 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125225 restraints weight = 52923.403| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.17 r_work: 0.3341 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36655 Z= 0.211 Angle : 0.602 14.413 49667 Z= 0.304 Chirality : 0.044 0.209 5698 Planarity : 0.004 0.055 6655 Dihedral : 4.532 59.399 5053 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 17.61 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.01 (0.12), residues: 4708 helix: 2.80 (0.13), residues: 1466 sheet: -1.30 (0.19), residues: 666 loop : 0.01 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG n 54 TYR 0.020 0.002 TYR i 42 PHE 0.017 0.002 PHE C 179 TRP 0.033 0.002 TRP C 6 HIS 0.004 0.001 HISAP 2 Details of bonding type rmsd covalent geometry : bond 0.00500 (36655) covalent geometry : angle 0.60242 (49667) hydrogen bonds : bond 0.05084 ( 1597) hydrogen bonds : angle 4.01594 ( 4590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 724 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 LYS cc_start: 0.8598 (tttt) cc_final: 0.7786 (tppt) REVERT: 0 81 ASN cc_start: 0.8513 (m-40) cc_final: 0.8294 (t0) REVERT: 0 156 ASN cc_start: 0.5682 (m-40) cc_final: 0.5420 (m-40) REVERT: 0 159 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7372 (tt) REVERT: 9 21 GLU cc_start: 0.7411 (tt0) cc_final: 0.7199 (tt0) REVERT: 9 40 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8215 (mtm-85) REVERT: 9 78 GLU cc_start: 0.8386 (tp30) cc_final: 0.7881 (tp30) REVERT: 9 85 LYS cc_start: 0.6251 (tttt) cc_final: 0.5063 (tmtt) REVERT: A 23 SER cc_start: 0.9372 (m) cc_final: 0.8966 (t) REVERT: AC 342 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7522 (pt0) REVERT: AE 356 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7784 (mtm) REVERT: AF 351 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7677 (tp-100) REVERT: AK 352 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4997 (m-30) REVERT: AM 330 ASN cc_start: 0.7223 (t0) cc_final: 0.6581 (t0) REVERT: AN 341 ASN cc_start: 0.8632 (m-40) cc_final: 0.8226 (m-40) REVERT: AN 357 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8077 (ttmm) REVERT: AO 331 MET cc_start: 0.8671 (mmm) cc_final: 0.8237 (ttm) REVERT: B 219 MET cc_start: 0.7495 (mtp) cc_final: 0.6820 (mtp) REVERT: C 140 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7612 (mm-30) REVERT: C 185 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9034 (mt) REVERT: C 259 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8461 (p0) REVERT: C 261 GLN cc_start: 0.8398 (tp40) cc_final: 0.8060 (mm-40) REVERT: AP 55 GLN cc_start: 0.8092 (tp40) cc_final: 0.7758 (tp40) REVERT: AP 98 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: AP 125 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8545 (mp0) REVERT: AP 262 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6679 (mp) REVERT: AQ 209 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7603 (pp) REVERT: AQ 216 ARG cc_start: 0.8481 (mmt180) cc_final: 0.8076 (mmt-90) REVERT: AQ 255 MET cc_start: 0.8771 (mmm) cc_final: 0.8321 (mmp) REVERT: AR 98 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4389 (tt0) REVERT: c 106 ASN cc_start: 0.9419 (t0) cc_final: 0.9011 (t0) REVERT: d 41 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.7860 (mmm-85) REVERT: d 47 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8381 (mmtm) REVERT: d 111 GLN cc_start: 0.9057 (tp40) cc_final: 0.8288 (tp40) REVERT: e 13 GLN cc_start: 0.8796 (tt0) cc_final: 0.8386 (mt0) REVERT: f 20 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7873 (pt0) REVERT: g 10 THR cc_start: 0.8325 (p) cc_final: 0.8070 (p) REVERT: g 105 MET cc_start: 0.8697 (mmm) cc_final: 0.8419 (mmm) REVERT: h 52 GLU cc_start: 0.8352 (mp0) cc_final: 0.7961 (mp0) REVERT: h 96 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8684 (mttm) REVERT: h 127 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8143 (mm-40) REVERT: h 131 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8023 (mmp-170) REVERT: h 134 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8310 (mm-40) REVERT: i 135 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5125 (ttp) REVERT: j 52 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8098 (tm-30) REVERT: j 80 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8235 (mt-10) REVERT: k 52 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7439 (tm-30) REVERT: k 91 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8076 (pt0) REVERT: m 112 MET cc_start: 0.7991 (mtm) cc_final: 0.7725 (mtp) REVERT: m 194 ASP cc_start: 0.8609 (t0) cc_final: 0.8124 (t0) REVERT: n 16 MET cc_start: 0.8710 (mmt) cc_final: 0.8315 (tpt) REVERT: n 158 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6067 (t80) REVERT: n 218 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8277 (mp) REVERT: o 158 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7334 (t80) REVERT: o 162 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: o 228 GLN cc_start: 0.8727 (mt0) cc_final: 0.8388 (mt0) REVERT: o 231 MET cc_start: 0.9074 (tpp) cc_final: 0.8799 (tpt) REVERT: p 142 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8000 (tpp-160) REVERT: p 162 ASP cc_start: 0.7728 (m-30) cc_final: 0.7243 (m-30) REVERT: p 163 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7950 (ttt-90) REVERT: q 16 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8056 (tpp) REVERT: q 65 ASN cc_start: 0.8821 (t0) cc_final: 0.8594 (t0) REVERT: q 200 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8260 (tm-30) REVERT: q 205 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: q 238 MET cc_start: 0.9029 (mtm) cc_final: 0.8469 (mtp) outliers start: 149 outliers final: 112 residues processed: 817 average time/residue: 0.2031 time to fit residues: 278.5555 Evaluate side-chains 842 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 714 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 TYR Chi-restraints excluded: chain 0 residue 28 PHE Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 139 VAL Chi-restraints excluded: chain 0 residue 151 LEU Chi-restraints excluded: chain 0 residue 159 ILE Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 104 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain AB residue 341 ASN Chi-restraints excluded: chain AC residue 349 ILE Chi-restraints excluded: chain AE residue 356 MET Chi-restraints excluded: chain AF residue 340 SER Chi-restraints excluded: chain AJ residue 335 ILE Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 330 ASN Chi-restraints excluded: chain AL residue 361 VAL Chi-restraints excluded: chain AM residue 332 VAL Chi-restraints excluded: chain AM residue 358 ASP Chi-restraints excluded: chain AO residue 332 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain AP residue 31 THR Chi-restraints excluded: chain AP residue 98 GLU Chi-restraints excluded: chain AP residue 127 THR Chi-restraints excluded: chain AP residue 148 ILE Chi-restraints excluded: chain AP residue 177 THR Chi-restraints excluded: chain AP residue 262 LEU Chi-restraints excluded: chain AQ residue 30 SER Chi-restraints excluded: chain AQ residue 72 SER Chi-restraints excluded: chain AQ residue 95 MET Chi-restraints excluded: chain AQ residue 209 LEU Chi-restraints excluded: chain AR residue 96 MET Chi-restraints excluded: chain AR residue 98 GLU Chi-restraints excluded: chain AR residue 104 GLN Chi-restraints excluded: chain AR residue 256 SER Chi-restraints excluded: chain AR residue 258 VAL Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 117 LEU Chi-restraints excluded: chain d residue 27 SER Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 128 MET Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 108 MET Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 135 MET Chi-restraints excluded: chain j residue 62 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 128 MET Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 242 SER Chi-restraints excluded: chain n residue 55 VAL Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 120 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 201 THR Chi-restraints excluded: chain n residue 218 LEU Chi-restraints excluded: chain o residue 49 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 64 HIS Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 114 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 168 LYS Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain p residue 130 THR Chi-restraints excluded: chain p residue 136 SER Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 181 LEU Chi-restraints excluded: chain q residue 197 VAL Chi-restraints excluded: chain q residue 205 GLU Chi-restraints excluded: chain q residue 241 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 275 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 209 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 343 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 268 optimal weight: 0.9990 chunk 310 optimal weight: 0.9980 chunk 407 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AJ 341 ASN AJ 355 GLN AN 342 GLN AO 351 GLN AO 355 GLN ** AQ 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 104 GLN b 29 ASN b 50 GLN b 101 ASN b 107 GLN ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN h 30 ASN h 46 HIS ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 46 HIS ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 120 GLN ** q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 125 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130999 restraints weight = 51987.724| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.22 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36655 Z= 0.108 Angle : 0.538 15.266 49667 Z= 0.270 Chirality : 0.040 0.214 5698 Planarity : 0.004 0.054 6655 Dihedral : 4.207 58.599 5053 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 2.52 % Allowed : 18.97 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 1.28 (0.12), residues: 4708 helix: 3.13 (0.13), residues: 1475 sheet: -1.27 (0.18), residues: 704 loop : 0.17 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG n 142 TYR 0.019 0.001 TYR 9 24 PHE 0.025 0.001 PHE n 225 TRP 0.031 0.001 TRP C 6 HIS 0.009 0.001 HIS h 46 Details of bonding type rmsd covalent geometry : bond 0.00242 (36655) covalent geometry : angle 0.53823 (49667) hydrogen bonds : bond 0.04162 ( 1597) hydrogen bonds : angle 3.70171 ( 4590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9595.17 seconds wall clock time: 165 minutes 5.16 seconds (9905.16 seconds total)