Starting phenix.real_space_refine on Fri Mar 6 06:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbb_24976/03_2026/7sbb_24976.map" } resolution = 3.1 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= 0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 113 5.16 5 C 18016 2.51 5 N 4970 2.21 5 O 5764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28938 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "C" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "G" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5593 Classifications: {'peptide': 680} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 651} Chain breaks: 6 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "K" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "X" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 713 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 10} Link IDs: {'rna2p': 5, 'rna3p': 27} Chain: "Z" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 20, 'rna3p': 22} Time building chain proxies: 6.27, per 1000 atoms: 0.22 Number of scatterers: 28938 At special positions: 0 Unit cell: (114.95, 123.31, 229.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 75 15.00 O 5764 8.00 N 4970 7.00 C 18016 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6424 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 34 sheets defined 46.5% alpha, 15.9% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 64 through 83 Proline residue: A 71 - end of helix removed outlier: 3.724A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.656A pdb=" N THR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.538A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 317 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.515A pdb=" N THR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.732A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.887A pdb=" N GLN C 68 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.891A pdb=" N ASP C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.516A pdb=" N GLY C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.976A pdb=" N GLN D 68 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 137 through 140 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.578A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 295 through 317 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 64 through 83 removed outlier: 3.926A pdb=" N GLN E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Proline residue: E 71 - end of helix removed outlier: 3.651A pdb=" N ALA E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 250 through 267 Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.771A pdb=" N GLN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 317 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 69 through 83 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.938A pdb=" N THR F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 317 removed outlier: 3.599A pdb=" N LEU F 299 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.514A pdb=" N LYS G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.631A pdb=" N THR G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 3.935A pdb=" N THR G 236 " --> pdb=" O ASN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 266 removed outlier: 3.518A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA G 259 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 removed outlier: 3.940A pdb=" N THR G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 288 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 317 removed outlier: 4.513A pdb=" N LYS G 301 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 43 Processing helix chain 'H' and resid 54 through 59 removed outlier: 4.068A pdb=" N ASN H 57 " --> pdb=" O VAL H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.617A pdb=" N ASN H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.182A pdb=" N ARG I 11 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.258A pdb=" N ALA I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU I 34 " --> pdb=" O PRO I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 96 removed outlier: 3.632A pdb=" N GLU I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.748A pdb=" N ARG I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.715A pdb=" N ASN I 139 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 154 removed outlier: 3.649A pdb=" N PHE I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 4.030A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.525A pdb=" N ALA I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 213 removed outlier: 4.021A pdb=" N ASP I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 201 - end of helix removed outlier: 3.569A pdb=" N HIS I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 210 " --> pdb=" O LEU I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.804A pdb=" N LEU I 221 " --> pdb=" O PRO I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 238 removed outlier: 6.364A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 269 removed outlier: 3.712A pdb=" N ASN I 257 " --> pdb=" O GLY I 253 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 316 removed outlier: 3.877A pdb=" N GLN I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 497 removed outlier: 3.807A pdb=" N ASP I 492 " --> pdb=" O GLN I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 518 removed outlier: 3.705A pdb=" N ILE I 511 " --> pdb=" O HIS I 507 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN I 512 " --> pdb=" O GLN I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 584 Processing helix chain 'I' and resid 590 through 595 Processing helix chain 'I' and resid 608 through 620 removed outlier: 3.638A pdb=" N GLU I 613 " --> pdb=" O PRO I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.569A pdb=" N VAL I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS I 632 " --> pdb=" O TRP I 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP I 634 " --> pdb=" O VAL I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 647 removed outlier: 3.568A pdb=" N LEU I 647 " --> pdb=" O LEU I 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 703 removed outlier: 4.815A pdb=" N LYS I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) Proline residue: I 691 - end of helix Proline residue: I 699 - end of helix Processing helix chain 'I' and resid 720 through 724 removed outlier: 3.924A pdb=" N GLU I 724 " --> pdb=" O ASP I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 739 removed outlier: 4.249A pdb=" N SER I 736 " --> pdb=" O ALA I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 745 through 747 No H-bonds generated for 'chain 'I' and resid 745 through 747' Processing helix chain 'I' and resid 748 through 764 Processing helix chain 'I' and resid 774 through 776 No H-bonds generated for 'chain 'I' and resid 774 through 776' Processing helix chain 'I' and resid 777 through 788 Processing helix chain 'I' and resid 790 through 803 Processing helix chain 'I' and resid 809 through 824 removed outlier: 3.942A pdb=" N THR I 814 " --> pdb=" O GLU I 810 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP I 817 " --> pdb=" O VAL I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 827 through 845 removed outlier: 3.643A pdb=" N VAL I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 851 through 855 Processing helix chain 'I' and resid 857 through 862 Processing helix chain 'I' and resid 862 through 875 Processing helix chain 'I' and resid 880 through 897 removed outlier: 4.368A pdb=" N LEU I 886 " --> pdb=" O GLU I 882 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 899 No H-bonds generated for 'chain 'I' and resid 898 through 899' Processing helix chain 'I' and resid 900 through 903 Processing helix chain 'I' and resid 904 through 909 removed outlier: 4.318A pdb=" N ASP I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'I' and resid 913 through 935 Processing helix chain 'I' and resid 944 through 974 removed outlier: 5.007A pdb=" N ASN I 953 " --> pdb=" O GLN I 949 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG I 954 " --> pdb=" O GLU I 950 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 removed outlier: 4.443A pdb=" N LYS J 4 " --> pdb=" O MET J 1 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 17 removed outlier: 3.648A pdb=" N TYR J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 51 through 68 removed outlier: 3.907A pdb=" N LEU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU J 57 " --> pdb=" O GLU J 53 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 84 through 105 Processing helix chain 'J' and resid 115 through 122 removed outlier: 3.504A pdb=" N GLN J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 145 removed outlier: 3.704A pdb=" N GLN J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 removed outlier: 5.257A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 28 through 33 Processing helix chain 'K' and resid 33 through 45 Processing helix chain 'K' and resid 51 through 68 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 84 through 106 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 122 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.243A pdb=" N LEU A 27 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 219 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 29 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 217 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN A 31 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 215 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.665A pdb=" N THR A 38 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.011A pdb=" N GLY A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 128 removed outlier: 6.915A pdb=" N TYR B 21 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 224 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 23 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 222 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 25 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 214 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 275 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.837A pdb=" N THR B 38 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 148 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.939A pdb=" N TYR C 21 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 224 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS C 23 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 222 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 25 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 214 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 275 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.818A pdb=" N THR C 38 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 148 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.937A pdb=" N TYR D 21 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE D 224 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS D 23 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE D 222 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 25 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 275 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 142 through 148 Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.489A pdb=" N LEU E 27 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU E 219 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS E 29 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN E 217 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 142 through 148 Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.492A pdb=" N LEU F 27 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU F 219 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N HIS F 29 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN F 217 " --> pdb=" O HIS F 29 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 275 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 44 through 48 Processing sheet with id=AC6, first strand: chain 'F' and resid 142 through 147 removed outlier: 4.456A pdb=" N ASN F 167 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 127 through 129 removed outlier: 6.534A pdb=" N LEU G 27 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU G 219 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS G 29 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN G 217 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU G 275 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.549A pdb=" N SER G 59 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 136 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 61 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 142 through 146 Processing sheet with id=AD1, first strand: chain 'H' and resid 80 through 82 removed outlier: 6.656A pdb=" N GLU H 135 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AD3, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AD4, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.566A pdb=" N PHE H 211 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL H 203 " --> pdb=" O PHE H 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 213 " --> pdb=" O ASN H 201 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN H 217 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE H 197 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP H 219 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN H 195 " --> pdb=" O ASP H 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.976A pdb=" N GLN H 222 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU H 229 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP H 224 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 273 through 278 removed outlier: 6.863A pdb=" N ILE I 283 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE I 277 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 673 through 677 removed outlier: 3.744A pdb=" N ALA I 673 " --> pdb=" O LEU I 601 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE I 597 " --> pdb=" O THR I 677 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.27 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4705 1.28 - 1.42: 8082 1.42 - 1.55: 16491 1.55 - 1.69: 202 1.69 - 1.82: 180 Bond restraints: 29660 Sorted by residual: bond pdb=" C TYR E 313 " pdb=" O TYR E 313 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.17e-02 7.31e+03 6.39e+01 bond pdb=" C TYR F 313 " pdb=" O TYR F 313 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.21e+01 bond pdb=" C TYR D 313 " pdb=" O TYR D 313 " ideal model delta sigma weight residual 1.237 1.145 0.091 1.16e-02 7.43e+03 6.21e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.237 1.150 0.087 1.17e-02 7.31e+03 5.49e+01 bond pdb=" CA ASN H 71 " pdb=" C ASN H 71 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.21e-02 6.83e+03 5.12e+01 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 37540 3.80 - 7.59: 2785 7.59 - 11.39: 128 11.39 - 15.18: 13 15.18 - 18.98: 1 Bond angle restraints: 40467 Sorted by residual: angle pdb=" N PHE I 285 " pdb=" CA PHE I 285 " pdb=" C PHE I 285 " ideal model delta sigma weight residual 110.32 91.34 18.98 1.59e+00 3.96e-01 1.42e+02 angle pdb=" CA ASP F 130 " pdb=" CB ASP F 130 " pdb=" CG ASP F 130 " ideal model delta sigma weight residual 112.60 122.48 -9.88 1.00e+00 1.00e+00 9.77e+01 angle pdb=" N GLY G 114 " pdb=" CA GLY G 114 " pdb=" C GLY G 114 " ideal model delta sigma weight residual 112.29 123.12 -10.83 1.12e+00 7.97e-01 9.36e+01 angle pdb=" CA ASP I 640 " pdb=" CB ASP I 640 " pdb=" CG ASP I 640 " ideal model delta sigma weight residual 112.60 122.23 -9.63 1.00e+00 1.00e+00 9.26e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 121.67 -9.07 1.00e+00 1.00e+00 8.22e+01 ... (remaining 40462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 17274 35.55 - 71.11: 573 71.11 - 106.66: 95 106.66 - 142.22: 6 142.22 - 177.77: 3 Dihedral angle restraints: 17951 sinusoidal: 7972 harmonic: 9979 Sorted by residual: dihedral pdb=" O4' U Z 3 " pdb=" C1' U Z 3 " pdb=" N1 U Z 3 " pdb=" C2 U Z 3 " ideal model delta sinusoidal sigma weight residual -160.00 -0.90 -159.10 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U Z 34 " pdb=" C1' U Z 34 " pdb=" N1 U Z 34 " pdb=" C2 U Z 34 " ideal model delta sinusoidal sigma weight residual 200.00 62.15 137.85 1 1.50e+01 4.44e-03 7.43e+01 dihedral pdb=" O4' U Z 35 " pdb=" C1' U Z 35 " pdb=" N1 U Z 35 " pdb=" C2 U Z 35 " ideal model delta sinusoidal sigma weight residual 200.00 73.45 126.55 1 1.50e+01 4.44e-03 6.81e+01 ... (remaining 17948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 3643 0.157 - 0.313: 765 0.313 - 0.470: 117 0.470 - 0.627: 29 0.627 - 0.784: 11 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA GLU A 228 " pdb=" N GLU A 228 " pdb=" C GLU A 228 " pdb=" CB GLU A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA GLU A 288 " pdb=" N GLU A 288 " pdb=" C GLU A 288 " pdb=" CB GLU A 288 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA GLU I 812 " pdb=" N GLU I 812 " pdb=" C GLU I 812 " pdb=" CB GLU I 812 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 4562 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G Z 25 " -0.025 2.00e-02 2.50e+03 1.16e-01 4.01e+02 pdb=" N9 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G Z 25 " 0.150 2.00e-02 2.50e+03 pdb=" N7 G Z 25 " 0.149 2.00e-02 2.50e+03 pdb=" C5 G Z 25 " -0.019 2.00e-02 2.50e+03 pdb=" C6 G Z 25 " -0.052 2.00e-02 2.50e+03 pdb=" O6 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" N1 G Z 25 " -0.017 2.00e-02 2.50e+03 pdb=" C2 G Z 25 " -0.055 2.00e-02 2.50e+03 pdb=" N2 G Z 25 " 0.258 2.00e-02 2.50e+03 pdb=" N3 G Z 25 " -0.147 2.00e-02 2.50e+03 pdb=" C4 G Z 25 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Z 34 " -0.263 2.00e-02 2.50e+03 1.28e-01 3.70e+02 pdb=" N1 U Z 34 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U Z 34 " 0.047 2.00e-02 2.50e+03 pdb=" O2 U Z 34 " 0.102 2.00e-02 2.50e+03 pdb=" N3 U Z 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U Z 34 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U Z 34 " -0.179 2.00e-02 2.50e+03 pdb=" C5 U Z 34 " 0.114 2.00e-02 2.50e+03 pdb=" C6 U Z 34 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 584 " 0.189 2.00e-02 2.50e+03 1.18e-01 3.46e+02 pdb=" CG TRP I 584 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP I 584 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP I 584 " -0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP I 584 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP I 584 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP I 584 " -0.166 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 584 " 0.143 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 584 " -0.090 2.00e-02 2.50e+03 pdb=" CH2 TRP I 584 " 0.153 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 23739 3.18 - 3.75: 46863 3.75 - 4.33: 66230 4.33 - 4.90: 107426 Nonbonded interactions: 244406 Sorted by model distance: nonbonded pdb=" CB SER E 144 " pdb=" OD1 ASP E 170 " model vdw 2.030 3.440 nonbonded pdb=" CG MET D 162 " pdb=" O2' A X 10 " model vdw 2.161 3.440 nonbonded pdb=" NE2 GLN G 8 " pdb=" OE1 GLU G 275 " model vdw 2.188 3.120 nonbonded pdb=" O LEU E 302 " pdb=" OG SER E 305 " model vdw 2.213 3.040 nonbonded pdb=" N PHE I 285 " pdb=" O PHE I 285 " model vdw 2.226 2.496 ... (remaining 244401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.660 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.013 0.094 29660 Z= 0.836 Angle : 2.086 18.976 40467 Z= 1.376 Chirality : 0.139 0.784 4565 Planarity : 0.021 0.251 4974 Dihedral : 18.010 177.772 11527 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Rotamer: Outliers : 3.53 % Allowed : 7.88 % Favored : 88.59 % Cbeta Deviations : 3.02 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3399 helix: -1.94 (0.11), residues: 1445 sheet: -0.42 (0.23), residues: 377 loop : -0.94 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 163 TYR 0.218 0.023 TYR I 497 PHE 0.084 0.013 PHE H 17 TRP 0.189 0.031 TRP I 584 HIS 0.027 0.005 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.01297 (29660) covalent geometry : angle 2.08598 (40467) hydrogen bonds : bond 0.19974 ( 1334) hydrogen bonds : angle 8.14840 ( 3811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1148 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8227 (m110) cc_final: 0.7489 (m110) REVERT: A 48 GLN cc_start: 0.8016 (tt0) cc_final: 0.7499 (tt0) REVERT: A 60 ARG cc_start: 0.8630 (ptp-110) cc_final: 0.8302 (ptp90) REVERT: A 65 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7905 (ttpp) REVERT: A 78 GLU cc_start: 0.7413 (tt0) cc_final: 0.7058 (tt0) REVERT: A 94 ASN cc_start: 0.8243 (p0) cc_final: 0.8019 (p0) REVERT: A 113 TYR cc_start: 0.8569 (m-80) cc_final: 0.8145 (m-80) REVERT: A 128 TYR cc_start: 0.7707 (m-10) cc_final: 0.7369 (m-10) REVERT: A 156 MET cc_start: 0.7853 (mmt) cc_final: 0.7568 (mmm) REVERT: A 170 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6815 (p0) REVERT: A 185 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7888 (ttm170) REVERT: A 186 ASP cc_start: 0.7176 (m-30) cc_final: 0.6922 (m-30) REVERT: A 190 GLU cc_start: 0.7511 (mp0) cc_final: 0.6891 (mp0) REVERT: A 216 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7961 (ttpp) REVERT: A 253 GLU cc_start: 0.7104 (tp30) cc_final: 0.6829 (tp30) REVERT: A 254 LEU cc_start: 0.8633 (tp) cc_final: 0.8242 (tp) REVERT: A 313 TYR cc_start: 0.8805 (t80) cc_final: 0.8447 (t80) REVERT: B 1 MET cc_start: 0.8090 (mmm) cc_final: 0.7837 (mmt) REVERT: B 18 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 78 GLU cc_start: 0.7176 (tt0) cc_final: 0.6922 (tt0) REVERT: B 82 ASN cc_start: 0.8017 (t0) cc_final: 0.7794 (t0) REVERT: B 123 GLU cc_start: 0.7482 (tp30) cc_final: 0.7212 (tp30) REVERT: B 130 ASP cc_start: 0.7139 (t0) cc_final: 0.6934 (t0) REVERT: B 148 ASN cc_start: 0.7519 (m-40) cc_final: 0.7299 (m110) REVERT: B 151 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 176 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (p) REVERT: B 190 GLU cc_start: 0.7759 (mp0) cc_final: 0.7224 (mp0) REVERT: B 198 ASN cc_start: 0.8430 (m-40) cc_final: 0.8110 (m-40) REVERT: B 212 THR cc_start: 0.8261 (m) cc_final: 0.7999 (t) REVERT: B 226 ASP cc_start: 0.6857 (p0) cc_final: 0.6376 (p0) REVERT: B 228 GLU cc_start: 0.7037 (pm20) cc_final: 0.6793 (pm20) REVERT: B 256 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 271 VAL cc_start: 0.8605 (m) cc_final: 0.7815 (t) REVERT: B 272 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7763 (mtm180) REVERT: B 287 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7560 (tp-100) REVERT: B 290 ASN cc_start: 0.8060 (m-40) cc_final: 0.7854 (m-40) REVERT: B 303 LEU cc_start: 0.8822 (mt) cc_final: 0.8615 (mp) REVERT: B 311 GLN cc_start: 0.8334 (tt0) cc_final: 0.8096 (tt0) REVERT: C 5 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8034 (mt) REVERT: C 18 SER cc_start: 0.8141 (m) cc_final: 0.7939 (p) REVERT: C 53 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6288 (pt0) REVERT: C 97 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 140 GLN cc_start: 0.7656 (pm20) cc_final: 0.7375 (mp10) REVERT: C 190 GLU cc_start: 0.7529 (mp0) cc_final: 0.6777 (mp0) REVERT: C 241 ASP cc_start: 0.7490 (t0) cc_final: 0.7220 (t0) REVERT: C 264 ASP cc_start: 0.6948 (t70) cc_final: 0.6726 (t0) REVERT: C 268 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8151 (mtmm) REVERT: C 271 VAL cc_start: 0.8769 (t) cc_final: 0.8536 (m) REVERT: C 272 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7493 (mtm180) REVERT: C 275 GLU cc_start: 0.6872 (tt0) cc_final: 0.6366 (tt0) REVERT: C 296 ASP cc_start: 0.7421 (t0) cc_final: 0.7209 (t0) REVERT: C 311 GLN cc_start: 0.8153 (tt0) cc_final: 0.7930 (tt0) REVERT: D 18 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8084 (p) REVERT: D 43 ASN cc_start: 0.7906 (m110) cc_final: 0.7695 (m-40) REVERT: D 68 GLN cc_start: 0.7557 (pt0) cc_final: 0.6672 (pt0) REVERT: D 82 ASN cc_start: 0.8125 (t0) cc_final: 0.7733 (t0) REVERT: D 90 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7870 (mmtt) REVERT: D 93 LYS cc_start: 0.8047 (tppt) cc_final: 0.7783 (tppt) REVERT: D 101 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6616 (mm-30) REVERT: D 123 GLU cc_start: 0.7426 (tp30) cc_final: 0.7117 (tp30) REVERT: D 126 LYS cc_start: 0.8232 (mttp) cc_final: 0.7812 (mttp) REVERT: D 139 GLU cc_start: 0.7263 (mp0) cc_final: 0.6884 (mp0) REVERT: D 167 ASN cc_start: 0.8248 (t0) cc_final: 0.7976 (t0) REVERT: D 215 MET cc_start: 0.7819 (mtp) cc_final: 0.7499 (mtm) REVERT: D 241 ASP cc_start: 0.8116 (t0) cc_final: 0.7851 (t0) REVERT: D 246 GLU cc_start: 0.6994 (pt0) cc_final: 0.6588 (pt0) REVERT: D 249 LYS cc_start: 0.8164 (mttt) cc_final: 0.7900 (mttt) REVERT: D 253 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6697 (tm-30) REVERT: D 256 GLU cc_start: 0.7200 (tt0) cc_final: 0.6910 (tt0) REVERT: D 269 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 21 TYR cc_start: 0.8109 (m-10) cc_final: 0.7870 (m-80) REVERT: E 31 GLN cc_start: 0.8301 (mm110) cc_final: 0.7875 (mm-40) REVERT: E 48 GLN cc_start: 0.7695 (tt0) cc_final: 0.7403 (tt0) REVERT: E 106 GLN cc_start: 0.8256 (mt0) cc_final: 0.7991 (mt0) REVERT: E 123 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6853 (mm-30) REVERT: E 146 THR cc_start: 0.7948 (p) cc_final: 0.7724 (t) REVERT: E 183 SER cc_start: 0.8009 (t) cc_final: 0.7771 (m) REVERT: E 190 GLU cc_start: 0.7510 (mp0) cc_final: 0.7160 (mp0) REVERT: E 200 LEU cc_start: 0.8477 (mt) cc_final: 0.8251 (mm) REVERT: E 226 ASP cc_start: 0.7019 (t0) cc_final: 0.5709 (t0) REVERT: E 231 SER cc_start: 0.8232 (t) cc_final: 0.7977 (p) REVERT: E 267 ASN cc_start: 0.8274 (m-40) cc_final: 0.8020 (m-40) REVERT: E 269 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6741 (mm-30) REVERT: E 283 ASP cc_start: 0.7562 (p0) cc_final: 0.7291 (p0) REVERT: E 286 LEU cc_start: 0.8443 (mp) cc_final: 0.8241 (mt) REVERT: E 287 GLN cc_start: 0.7543 (tp40) cc_final: 0.7188 (tp40) REVERT: E 288 GLU cc_start: 0.7062 (pt0) cc_final: 0.6804 (pt0) REVERT: E 290 ASN cc_start: 0.7906 (p0) cc_final: 0.7558 (p0) REVERT: E 291 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7206 (p0) REVERT: E 309 GLN cc_start: 0.8446 (mt0) cc_final: 0.7739 (mt0) REVERT: F 48 GLN cc_start: 0.7904 (tt0) cc_final: 0.7660 (tt0) REVERT: F 59 SER cc_start: 0.8484 (m) cc_final: 0.8057 (p) REVERT: F 66 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: F 72 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: F 126 LYS cc_start: 0.8462 (mttp) cc_final: 0.8195 (mttp) REVERT: F 138 TYR cc_start: 0.8221 (t80) cc_final: 0.7946 (t80) REVERT: F 175 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6562 (mt-10) REVERT: F 180 THR cc_start: 0.7920 (m) cc_final: 0.7533 (p) REVERT: F 226 ASP cc_start: 0.7141 (p0) cc_final: 0.6934 (p0) REVERT: F 232 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7801 (m110) REVERT: F 249 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7754 (mmmt) REVERT: F 253 GLU cc_start: 0.7239 (tm-30) cc_final: 0.7020 (tm-30) REVERT: F 295 ASN cc_start: 0.7640 (m-40) cc_final: 0.7244 (t0) REVERT: F 298 GLU cc_start: 0.7346 (mp0) cc_final: 0.6622 (mp0) REVERT: F 301 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7979 (ttmm) REVERT: G 10 GLN cc_start: 0.7284 (mt0) cc_final: 0.7044 (mt0) REVERT: G 18 SER cc_start: 0.7665 (p) cc_final: 0.7407 (p) REVERT: G 24 PHE cc_start: 0.8152 (m-80) cc_final: 0.7942 (m-80) REVERT: G 25 LEU cc_start: 0.7986 (mp) cc_final: 0.7673 (mp) REVERT: G 77 ARG cc_start: 0.6687 (mtp85) cc_final: 0.5868 (mtp85) REVERT: G 119 ASP cc_start: 0.6797 (t0) cc_final: 0.6537 (t70) REVERT: G 124 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7363 (ttm110) REVERT: G 133 PHE cc_start: 0.7731 (m-80) cc_final: 0.7435 (m-80) REVERT: G 162 MET cc_start: -0.1396 (tpp) cc_final: -0.1652 (tpp) REVERT: G 182 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6607 (mt-10) REVERT: G 194 TYR cc_start: 0.7866 (t80) cc_final: 0.7373 (t80) REVERT: G 216 LYS cc_start: 0.8052 (tppt) cc_final: 0.7641 (tppt) REVERT: G 239 LEU cc_start: 0.8412 (tp) cc_final: 0.7848 (tp) REVERT: G 243 MET cc_start: 0.6935 (mtm) cc_final: 0.6369 (mtm) REVERT: G 251 ILE cc_start: 0.7371 (mm) cc_final: 0.7118 (mm) REVERT: G 288 GLU cc_start: 0.7513 (tp30) cc_final: 0.6955 (tp30) REVERT: H 136 PHE cc_start: 0.8528 (m-80) cc_final: 0.8255 (m-80) REVERT: H 180 TYR cc_start: 0.8473 (p90) cc_final: 0.8257 (p90) REVERT: H 195 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7229 (mm-40) REVERT: H 222 GLN cc_start: 0.7473 (tp40) cc_final: 0.6881 (tp40) REVERT: H 228 PHE cc_start: 0.8557 (m-80) cc_final: 0.7841 (m-80) REVERT: I 36 PHE cc_start: 0.7325 (m-10) cc_final: 0.6978 (m-10) REVERT: I 82 ILE cc_start: 0.9105 (mm) cc_final: 0.8755 (mt) REVERT: I 83 LEU cc_start: 0.8740 (tp) cc_final: 0.8532 (tp) REVERT: I 105 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7393 (mtp85) REVERT: I 205 LEU cc_start: 0.7665 (mp) cc_final: 0.7434 (mm) REVERT: I 211 VAL cc_start: 0.8438 (p) cc_final: 0.7659 (m) REVERT: I 245 TYR cc_start: 0.7966 (p90) cc_final: 0.7692 (p90) REVERT: I 275 LEU cc_start: 0.8472 (tp) cc_final: 0.8214 (tp) REVERT: I 285 PHE cc_start: 0.7430 (m-80) cc_final: 0.7175 (m-80) REVERT: I 291 GLU cc_start: 0.7847 (pm20) cc_final: 0.7456 (pm20) REVERT: I 297 GLU cc_start: 0.7405 (pt0) cc_final: 0.6299 (pt0) REVERT: I 298 ILE cc_start: 0.8885 (mt) cc_final: 0.8431 (tp) REVERT: I 490 PHE cc_start: 0.8505 (t80) cc_final: 0.8289 (t80) REVERT: I 495 ASP cc_start: 0.7579 (m-30) cc_final: 0.7230 (m-30) REVERT: I 507 HIS cc_start: 0.7660 (p-80) cc_final: 0.7406 (p-80) REVERT: I 511 ILE cc_start: 0.8221 (mm) cc_final: 0.7709 (mt) REVERT: I 512 GLN cc_start: 0.7328 (tp40) cc_final: 0.6939 (tt0) REVERT: I 516 ASN cc_start: 0.7466 (m-40) cc_final: 0.7215 (m-40) REVERT: I 574 SER cc_start: 0.8614 (t) cc_final: 0.8041 (p) REVERT: I 612 VAL cc_start: 0.8837 (m) cc_final: 0.8605 (t) REVERT: I 635 VAL cc_start: 0.8866 (p) cc_final: 0.8646 (m) REVERT: I 638 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7995 (mmmt) REVERT: I 663 LYS cc_start: 0.7763 (pttt) cc_final: 0.7394 (pttt) REVERT: I 664 TYR cc_start: 0.7824 (m-80) cc_final: 0.7537 (m-80) REVERT: I 690 LYS cc_start: 0.8455 (mttt) cc_final: 0.8133 (mttt) REVERT: I 707 ILE cc_start: 0.8395 (tt) cc_final: 0.8112 (pt) REVERT: I 740 ILE cc_start: 0.8758 (tp) cc_final: 0.8508 (mt) REVERT: I 746 VAL cc_start: 0.8647 (p) cc_final: 0.8353 (p) REVERT: I 784 GLU cc_start: 0.7071 (pt0) cc_final: 0.6842 (pt0) REVERT: I 818 GLN cc_start: 0.7829 (mt0) cc_final: 0.7366 (mt0) REVERT: I 830 MET cc_start: 0.7031 (mtm) cc_final: 0.6595 (mtm) REVERT: I 832 GLU cc_start: 0.7553 (tp30) cc_final: 0.7344 (tp30) REVERT: I 848 TYR cc_start: 0.8721 (t80) cc_final: 0.8408 (t80) REVERT: I 871 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: I 901 VAL cc_start: 0.8712 (t) cc_final: 0.8422 (p) REVERT: I 912 VAL cc_start: 0.8886 (t) cc_final: 0.8666 (p) REVERT: I 914 TYR cc_start: 0.7757 (t80) cc_final: 0.7279 (t80) REVERT: I 936 LEU cc_start: 0.8496 (tp) cc_final: 0.8125 (tp) REVERT: I 939 GLU cc_start: 0.7194 (tp30) cc_final: 0.6939 (tp30) REVERT: I 942 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8521 (mmmt) REVERT: I 954 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7510 (ptp90) REVERT: I 960 GLU cc_start: 0.7262 (tt0) cc_final: 0.7017 (tt0) REVERT: J 1 MET cc_start: -0.0990 (mmm) cc_final: -0.1190 (mmm) REVERT: J 53 GLU cc_start: 0.7189 (mp0) cc_final: 0.6689 (mp0) REVERT: J 63 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7568 (tp) REVERT: J 92 GLU cc_start: 0.8046 (tp30) cc_final: 0.7601 (tp30) REVERT: J 94 GLU cc_start: 0.7522 (pt0) cc_final: 0.7255 (pt0) REVERT: J 105 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6819 (ptp90) REVERT: J 128 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8130 (p) REVERT: K 63 LEU cc_start: 0.8545 (tp) cc_final: 0.8318 (tp) REVERT: K 67 LEU cc_start: 0.7928 (mp) cc_final: 0.7597 (mp) REVERT: K 94 GLU cc_start: 0.7674 (tp30) cc_final: 0.6989 (tp30) REVERT: K 110 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6845 (tm-30) outliers start: 105 outliers final: 28 residues processed: 1197 average time/residue: 0.2232 time to fit residues: 403.2442 Evaluate side-chains 1035 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 990 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 685 THR Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 802 ARG Chi-restraints excluded: chain I residue 871 GLN Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 954 ARG Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 171 HIS A 198 ASN A 218 HIS A 295 ASN B 10 GLN B 43 ASN B 99 ASN B 171 HIS B 217 ASN B 242 GLN B 309 GLN C 43 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 281 HIS D 31 GLN D 68 GLN D 99 ASN D 208 GLN D 217 ASN D 267 ASN D 308 GLN E 8 GLN E 48 GLN E 68 GLN E 82 ASN E 140 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 232 ASN E 242 GLN ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN F 106 GLN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 287 GLN G 20 HIS G 99 ASN H 70 GLN H 95 ASN H 143 GLN I 84 ASN I 219 HIS I 235 ASN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 GLN I 488 GLN I 636 ASN I 651 ASN I 754 ASN I 849 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 891 GLN I 951 GLN J 62 GLN J 146 ASN K 89 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114835 restraints weight = 44138.044| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.02 r_work: 0.3346 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29660 Z= 0.212 Angle : 0.800 10.777 40467 Z= 0.419 Chirality : 0.050 0.421 4565 Planarity : 0.005 0.077 4974 Dihedral : 16.131 177.589 5018 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 3.80 % Allowed : 13.33 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3399 helix: -0.11 (0.13), residues: 1494 sheet: -0.05 (0.24), residues: 401 loop : -0.89 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 201 TYR 0.029 0.002 TYR I 844 PHE 0.025 0.002 PHE E 151 TRP 0.025 0.002 TRP K 50 HIS 0.013 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00461 (29660) covalent geometry : angle 0.79958 (40467) hydrogen bonds : bond 0.04978 ( 1334) hydrogen bonds : angle 5.13789 ( 3811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1010 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7261 (tpp) cc_final: 0.7038 (mmt) REVERT: A 21 TYR cc_start: 0.8815 (m-80) cc_final: 0.8558 (m-80) REVERT: A 45 THR cc_start: 0.8596 (t) cc_final: 0.8376 (p) REVERT: A 57 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7739 (mm-40) REVERT: A 78 GLU cc_start: 0.8261 (tt0) cc_final: 0.8028 (tt0) REVERT: A 82 ASN cc_start: 0.8807 (t0) cc_final: 0.8528 (t0) REVERT: A 94 ASN cc_start: 0.8303 (p0) cc_final: 0.8022 (p0) REVERT: A 156 MET cc_start: 0.8055 (mmt) cc_final: 0.7740 (mmm) REVERT: A 166 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 168 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 182 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 253 GLU cc_start: 0.8075 (tp30) cc_final: 0.7563 (tp30) REVERT: A 272 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7912 (ttt180) REVERT: A 313 TYR cc_start: 0.8810 (t80) cc_final: 0.8580 (t80) REVERT: B 53 GLU cc_start: 0.7602 (tp30) cc_final: 0.7040 (tp30) REVERT: B 87 SER cc_start: 0.8690 (t) cc_final: 0.8328 (t) REVERT: B 89 ASP cc_start: 0.7987 (p0) cc_final: 0.7700 (p0) REVERT: B 123 GLU cc_start: 0.7840 (tp30) cc_final: 0.7502 (tp30) REVERT: B 190 GLU cc_start: 0.8247 (mp0) cc_final: 0.8018 (mp0) REVERT: B 212 THR cc_start: 0.8243 (m) cc_final: 0.7945 (t) REVERT: B 226 ASP cc_start: 0.7385 (p0) cc_final: 0.6894 (p0) REVERT: B 253 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 256 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 268 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8448 (mtmm) REVERT: B 272 ARG cc_start: 0.8530 (mtm180) cc_final: 0.8228 (mtm180) REVERT: B 273 LYS cc_start: 0.8573 (mttp) cc_final: 0.8316 (mmtm) REVERT: B 298 GLU cc_start: 0.7975 (tp30) cc_final: 0.7731 (tp30) REVERT: B 308 GLN cc_start: 0.8637 (tp40) cc_final: 0.7844 (tp-100) REVERT: B 312 ASP cc_start: 0.8307 (m-30) cc_final: 0.7786 (m-30) REVERT: C 1 MET cc_start: 0.8041 (tpt) cc_final: 0.7550 (tpt) REVERT: C 5 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (mt) REVERT: C 6 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8514 (mtmt) REVERT: C 18 SER cc_start: 0.8318 (m) cc_final: 0.8064 (p) REVERT: C 53 GLU cc_start: 0.7629 (pt0) cc_final: 0.6985 (pt0) REVERT: C 54 LYS cc_start: 0.8349 (mptt) cc_final: 0.7984 (mptt) REVERT: C 89 ASP cc_start: 0.7869 (m-30) cc_final: 0.7583 (m-30) REVERT: C 95 LEU cc_start: 0.8939 (tp) cc_final: 0.8701 (tp) REVERT: C 161 VAL cc_start: 0.8381 (p) cc_final: 0.8103 (m) REVERT: C 216 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8167 (tttt) REVERT: C 226 ASP cc_start: 0.7706 (t0) cc_final: 0.7367 (t0) REVERT: C 241 ASP cc_start: 0.8409 (t0) cc_final: 0.8180 (t0) REVERT: C 246 GLU cc_start: 0.8067 (pt0) cc_final: 0.7656 (pt0) REVERT: C 249 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8651 (mtmm) REVERT: C 264 ASP cc_start: 0.7957 (t70) cc_final: 0.7622 (t0) REVERT: C 268 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8552 (mtmt) REVERT: C 275 GLU cc_start: 0.7729 (tt0) cc_final: 0.7326 (tt0) REVERT: C 288 GLU cc_start: 0.8049 (tt0) cc_final: 0.7316 (tt0) REVERT: C 303 LEU cc_start: 0.8881 (mt) cc_final: 0.8661 (mp) REVERT: C 311 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: C 316 GLU cc_start: 0.7962 (tp30) cc_final: 0.7602 (tp30) REVERT: C 317 PHE cc_start: 0.9002 (m-80) cc_final: 0.8725 (m-80) REVERT: D 78 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7731 (tt0) REVERT: D 93 LYS cc_start: 0.8285 (tppt) cc_final: 0.7967 (tppt) REVERT: D 101 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7426 (mm-30) REVERT: D 127 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8425 (t) REVERT: D 168 GLU cc_start: 0.8346 (pt0) cc_final: 0.8081 (pt0) REVERT: D 215 MET cc_start: 0.8162 (mtp) cc_final: 0.7820 (mtt) REVERT: D 243 MET cc_start: 0.8841 (ttm) cc_final: 0.8527 (mtp) REVERT: D 246 GLU cc_start: 0.7890 (pt0) cc_final: 0.7352 (pt0) REVERT: D 247 LEU cc_start: 0.8365 (pt) cc_final: 0.8111 (pp) REVERT: D 249 LYS cc_start: 0.8394 (mttt) cc_final: 0.8071 (mttt) REVERT: D 253 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 256 GLU cc_start: 0.8125 (tt0) cc_final: 0.7853 (tt0) REVERT: D 269 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7854 (mm-30) REVERT: D 298 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8017 (mt-10) REVERT: E 31 GLN cc_start: 0.8671 (mm110) cc_final: 0.8413 (mm110) REVERT: E 72 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: E 123 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7350 (mm-30) REVERT: E 162 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5545 (pmt) REVERT: E 183 SER cc_start: 0.8391 (t) cc_final: 0.8183 (m) REVERT: E 186 ASP cc_start: 0.7635 (p0) cc_final: 0.7385 (p0) REVERT: E 190 GLU cc_start: 0.7834 (mp0) cc_final: 0.7262 (mp0) REVERT: E 205 TYR cc_start: 0.7935 (m-80) cc_final: 0.7488 (m-80) REVERT: E 226 ASP cc_start: 0.7677 (t0) cc_final: 0.7282 (t0) REVERT: E 249 LYS cc_start: 0.8141 (mmpt) cc_final: 0.7923 (mmpt) REVERT: E 267 ASN cc_start: 0.8522 (m-40) cc_final: 0.8290 (m-40) REVERT: E 269 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 288 GLU cc_start: 0.7518 (pt0) cc_final: 0.7106 (pt0) REVERT: E 291 ASP cc_start: 0.7520 (p0) cc_final: 0.7223 (p0) REVERT: F 59 SER cc_start: 0.8695 (m) cc_final: 0.8191 (p) REVERT: F 66 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8226 (mtt90) REVERT: F 72 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: F 97 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7332 (mt-10) REVERT: F 138 TYR cc_start: 0.8317 (t80) cc_final: 0.8114 (t80) REVERT: F 180 THR cc_start: 0.8356 (m) cc_final: 0.8155 (p) REVERT: F 190 GLU cc_start: 0.7811 (mp0) cc_final: 0.7175 (mp0) REVERT: F 209 GLU cc_start: 0.8060 (tt0) cc_final: 0.7681 (tt0) REVERT: F 215 MET cc_start: 0.8267 (mtm) cc_final: 0.7931 (mtt) REVERT: F 249 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8075 (mmmt) REVERT: F 295 ASN cc_start: 0.8165 (m-40) cc_final: 0.7647 (t0) REVERT: F 298 GLU cc_start: 0.8231 (mp0) cc_final: 0.7692 (mp0) REVERT: G 6 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (ttpt) REVERT: G 8 GLN cc_start: 0.8458 (mt0) cc_final: 0.8051 (mt0) REVERT: G 25 LEU cc_start: 0.8151 (mp) cc_final: 0.7807 (mp) REVERT: G 72 GLU cc_start: 0.7639 (mp0) cc_final: 0.7234 (mp0) REVERT: G 77 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6390 (mtp85) REVERT: G 106 GLN cc_start: 0.8307 (pt0) cc_final: 0.8016 (pt0) REVERT: G 123 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7451 (tm-30) REVERT: G 124 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7912 (ttm110) REVERT: G 162 MET cc_start: -0.1660 (tpp) cc_final: -0.2575 (tpp) REVERT: G 177 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7921 (p) REVERT: G 182 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7954 (mt-10) REVERT: G 194 TYR cc_start: 0.8347 (t80) cc_final: 0.7736 (t80) REVERT: G 216 LYS cc_start: 0.8227 (tppt) cc_final: 0.7832 (tppt) REVERT: G 239 LEU cc_start: 0.8666 (tp) cc_final: 0.8209 (tp) REVERT: G 243 MET cc_start: 0.7494 (mtm) cc_final: 0.7258 (mtm) REVERT: G 260 THR cc_start: 0.8417 (t) cc_final: 0.8181 (p) REVERT: G 268 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7423 (mtmt) REVERT: G 288 GLU cc_start: 0.8182 (tp30) cc_final: 0.7567 (tp30) REVERT: H 20 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.8062 (ptp-110) REVERT: H 25 LEU cc_start: 0.8740 (tt) cc_final: 0.8443 (tp) REVERT: H 47 ILE cc_start: 0.8880 (mt) cc_final: 0.8659 (mt) REVERT: H 59 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8098 (mm110) REVERT: H 68 ARG cc_start: 0.8614 (mtp180) cc_final: 0.8255 (mtp180) REVERT: H 69 GLU cc_start: 0.8042 (mp0) cc_final: 0.7814 (mp0) REVERT: H 135 GLU cc_start: 0.8098 (pt0) cc_final: 0.7887 (pt0) REVERT: H 136 PHE cc_start: 0.8783 (m-80) cc_final: 0.8567 (m-80) REVERT: H 196 GLN cc_start: 0.8367 (pt0) cc_final: 0.8112 (pt0) REVERT: H 217 GLN cc_start: 0.7980 (tt0) cc_final: 0.7549 (tt0) REVERT: H 228 PHE cc_start: 0.8782 (m-80) cc_final: 0.8505 (m-80) REVERT: I 34 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7433 (mm-30) REVERT: I 84 ASN cc_start: 0.8006 (m-40) cc_final: 0.7445 (m-40) REVERT: I 235 ASN cc_start: 0.8475 (t0) cc_final: 0.8201 (t0) REVERT: I 261 ASN cc_start: 0.8236 (m-40) cc_final: 0.7998 (m110) REVERT: I 284 TYR cc_start: 0.7954 (m-80) cc_final: 0.7393 (m-80) REVERT: I 298 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8561 (tp) REVERT: I 497 TYR cc_start: 0.7674 (m-80) cc_final: 0.7468 (m-80) REVERT: I 499 GLU cc_start: 0.7914 (tp30) cc_final: 0.7498 (tp30) REVERT: I 512 GLN cc_start: 0.7924 (tp40) cc_final: 0.7226 (tm-30) REVERT: I 574 SER cc_start: 0.8870 (t) cc_final: 0.8351 (p) REVERT: I 577 MET cc_start: 0.7700 (tpt) cc_final: 0.7450 (tpt) REVERT: I 581 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: I 620 TYR cc_start: 0.8289 (m-80) cc_final: 0.7270 (m-80) REVERT: I 638 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8241 (mmmt) REVERT: I 639 MET cc_start: 0.7854 (mmp) cc_final: 0.7489 (mmp) REVERT: I 667 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7420 (mm-30) REVERT: I 668 ASP cc_start: 0.7193 (p0) cc_final: 0.6986 (p0) REVERT: I 690 LYS cc_start: 0.8816 (mttt) cc_final: 0.8585 (mttt) REVERT: I 705 LYS cc_start: 0.8523 (mttm) cc_final: 0.8299 (mttm) REVERT: I 707 ILE cc_start: 0.8785 (tt) cc_final: 0.8463 (pt) REVERT: I 746 VAL cc_start: 0.8599 (p) cc_final: 0.8385 (p) REVERT: I 776 GLN cc_start: 0.8127 (mp10) cc_final: 0.7762 (mm-40) REVERT: I 783 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7623 (tm-30) REVERT: I 818 GLN cc_start: 0.8560 (mt0) cc_final: 0.8188 (mt0) REVERT: I 830 MET cc_start: 0.8107 (mtm) cc_final: 0.7906 (mtm) REVERT: I 832 GLU cc_start: 0.8406 (tp30) cc_final: 0.8068 (tp30) REVERT: I 833 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8428 (ttmm) REVERT: I 859 HIS cc_start: 0.8760 (t70) cc_final: 0.8258 (t70) REVERT: I 870 GLU cc_start: 0.7873 (tp30) cc_final: 0.7455 (tp30) REVERT: I 900 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: I 901 VAL cc_start: 0.8842 (t) cc_final: 0.8575 (p) REVERT: I 909 ASP cc_start: 0.7712 (p0) cc_final: 0.7439 (p0) REVERT: I 914 TYR cc_start: 0.8003 (t80) cc_final: 0.7491 (t80) REVERT: I 920 GLN cc_start: 0.8388 (mt0) cc_final: 0.8026 (mt0) REVERT: I 923 GLU cc_start: 0.7845 (pp20) cc_final: 0.7575 (pp20) REVERT: I 971 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: J 5 LEU cc_start: 0.5299 (pp) cc_final: 0.4341 (pt) REVERT: J 63 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7825 (tt) REVERT: J 86 GLU cc_start: 0.7618 (pm20) cc_final: 0.7307 (pm20) REVERT: J 88 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7309 (ttp-170) REVERT: J 90 LEU cc_start: 0.8248 (tt) cc_final: 0.7936 (tt) REVERT: J 92 GLU cc_start: 0.8204 (tp30) cc_final: 0.7769 (tp30) REVERT: J 94 GLU cc_start: 0.8110 (pt0) cc_final: 0.7665 (pt0) REVERT: J 101 THR cc_start: 0.8830 (t) cc_final: 0.8573 (p) REVERT: J 105 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7598 (mtp85) REVERT: J 110 GLU cc_start: 0.8105 (tp30) cc_final: 0.7399 (tp30) REVERT: J 120 GLN cc_start: 0.8490 (tp40) cc_final: 0.8004 (tt0) REVERT: J 128 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8467 (p) REVERT: K 13 GLU cc_start: 0.7323 (tt0) cc_final: 0.7044 (tt0) REVERT: K 34 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6824 (tp) REVERT: K 41 GLU cc_start: 0.7237 (tp30) cc_final: 0.6658 (tp30) REVERT: K 52 GLU cc_start: 0.7845 (pp20) cc_final: 0.7350 (pp20) REVERT: K 55 LEU cc_start: 0.7782 (tt) cc_final: 0.7529 (tp) REVERT: K 71 GLU cc_start: 0.7427 (pm20) cc_final: 0.6853 (pm20) REVERT: K 94 GLU cc_start: 0.7871 (tp30) cc_final: 0.7159 (tp30) outliers start: 113 outliers final: 49 residues processed: 1055 average time/residue: 0.2098 time to fit residues: 336.9482 Evaluate side-chains 1035 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 966 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 308 GLN Chi-restraints excluded: chain I residue 581 GLN Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 685 THR Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 132 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 179 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 232 optimal weight: 0.3980 chunk 218 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 281 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 217 ASN B 43 ASN B 82 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN B 281 HIS ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 217 ASN D 290 ASN E 48 GLN E 82 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN E 294 GLN F 48 GLN F 198 ASN F 232 ASN H 95 ASN H 195 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 204 HIS ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 887 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115814 restraints weight = 44296.828| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.89 r_work: 0.3345 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29660 Z= 0.173 Angle : 0.696 9.824 40467 Z= 0.363 Chirality : 0.045 0.374 4565 Planarity : 0.005 0.058 4974 Dihedral : 15.747 177.846 4974 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.01 % Allowed : 16.43 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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 (0.14), residues: 3399 helix: 0.54 (0.13), residues: 1499 sheet: 0.06 (0.24), residues: 392 loop : -0.83 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG I 802 TYR 0.027 0.002 TYR I 844 PHE 0.026 0.002 PHE E 151 TRP 0.032 0.002 TRP I 154 HIS 0.012 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00379 (29660) covalent geometry : angle 0.69598 (40467) hydrogen bonds : bond 0.04236 ( 1334) hydrogen bonds : angle 4.76569 ( 3811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 987 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8830 (m-80) cc_final: 0.8533 (m-80) REVERT: A 43 ASN cc_start: 0.8600 (m110) cc_final: 0.8255 (m-40) REVERT: A 78 GLU cc_start: 0.8232 (tt0) cc_final: 0.7969 (tt0) REVERT: A 142 HIS cc_start: 0.8808 (p-80) cc_final: 0.8236 (p-80) REVERT: A 155 THR cc_start: 0.7651 (m) cc_final: 0.7309 (t) REVERT: A 166 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (tp) REVERT: A 168 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 253 GLU cc_start: 0.8068 (tp30) cc_final: 0.7511 (tp30) REVERT: A 272 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7887 (ttt180) REVERT: A 290 ASN cc_start: 0.8421 (m-40) cc_final: 0.7989 (m-40) REVERT: B 99 ASN cc_start: 0.8530 (m110) cc_final: 0.8290 (m-40) REVERT: B 123 GLU cc_start: 0.7780 (tp30) cc_final: 0.7414 (tp30) REVERT: B 190 GLU cc_start: 0.8254 (mp0) cc_final: 0.7902 (mp0) REVERT: B 226 ASP cc_start: 0.7438 (p0) cc_final: 0.7025 (p0) REVERT: B 253 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 256 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 268 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8476 (mtmm) REVERT: B 272 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8197 (mtm180) REVERT: B 287 GLN cc_start: 0.8298 (tp40) cc_final: 0.8063 (tp40) REVERT: B 288 GLU cc_start: 0.8215 (tt0) cc_final: 0.7861 (tt0) REVERT: B 298 GLU cc_start: 0.7996 (tp30) cc_final: 0.7750 (tp30) REVERT: B 308 GLN cc_start: 0.8682 (tp40) cc_final: 0.8346 (tp40) REVERT: C 1 MET cc_start: 0.7895 (tpt) cc_final: 0.7399 (tpt) REVERT: C 2 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7541 (mp) REVERT: C 5 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 6 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8473 (mtmt) REVERT: C 18 SER cc_start: 0.8331 (m) cc_final: 0.8104 (p) REVERT: C 53 GLU cc_start: 0.7590 (pt0) cc_final: 0.7281 (pt0) REVERT: C 89 ASP cc_start: 0.7873 (m-30) cc_final: 0.7576 (m-30) REVERT: C 95 LEU cc_start: 0.8872 (tp) cc_final: 0.8643 (tp) REVERT: C 152 GLU cc_start: 0.7799 (tt0) cc_final: 0.7573 (tt0) REVERT: C 161 VAL cc_start: 0.8422 (p) cc_final: 0.8187 (m) REVERT: C 180 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 226 ASP cc_start: 0.7847 (t0) cc_final: 0.7587 (t0) REVERT: C 241 ASP cc_start: 0.8417 (t0) cc_final: 0.8207 (t0) REVERT: C 246 GLU cc_start: 0.7975 (pt0) cc_final: 0.7423 (pt0) REVERT: C 249 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8631 (mtmm) REVERT: C 264 ASP cc_start: 0.7982 (t70) cc_final: 0.7660 (t0) REVERT: C 268 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8509 (mtmm) REVERT: C 269 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7750 (mm-30) REVERT: C 275 GLU cc_start: 0.7779 (tt0) cc_final: 0.7431 (tt0) REVERT: C 288 GLU cc_start: 0.8036 (tt0) cc_final: 0.7450 (tt0) REVERT: C 302 LEU cc_start: 0.8900 (tp) cc_final: 0.8690 (mp) REVERT: C 303 LEU cc_start: 0.8859 (mt) cc_final: 0.8636 (mp) REVERT: C 316 GLU cc_start: 0.8047 (tp30) cc_final: 0.7752 (tp30) REVERT: C 317 PHE cc_start: 0.8989 (m-80) cc_final: 0.8683 (m-80) REVERT: D 93 LYS cc_start: 0.8302 (tppt) cc_final: 0.7976 (tppt) REVERT: D 127 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8415 (t) REVERT: D 190 GLU cc_start: 0.7929 (mp0) cc_final: 0.7276 (mp0) REVERT: D 215 MET cc_start: 0.8213 (mtp) cc_final: 0.7900 (mtt) REVERT: D 243 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8385 (mtp) REVERT: D 246 GLU cc_start: 0.7858 (pt0) cc_final: 0.7315 (pt0) REVERT: D 249 LYS cc_start: 0.8355 (mttt) cc_final: 0.8084 (mttt) REVERT: D 253 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 256 GLU cc_start: 0.8106 (tt0) cc_final: 0.7863 (tt0) REVERT: D 269 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 31 GLN cc_start: 0.8613 (mm110) cc_final: 0.8293 (mm110) REVERT: E 46 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: E 104 CYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7183 (p) REVERT: E 123 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7274 (mm-30) REVERT: E 146 THR cc_start: 0.8423 (p) cc_final: 0.8210 (t) REVERT: E 182 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7485 (tm-30) REVERT: E 183 SER cc_start: 0.8348 (t) cc_final: 0.8031 (m) REVERT: E 186 ASP cc_start: 0.7530 (p0) cc_final: 0.7251 (p0) REVERT: E 190 GLU cc_start: 0.7745 (mp0) cc_final: 0.7080 (mp0) REVERT: E 205 TYR cc_start: 0.7849 (m-80) cc_final: 0.7149 (m-80) REVERT: E 226 ASP cc_start: 0.7655 (t0) cc_final: 0.7282 (t0) REVERT: E 253 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7200 (tm-30) REVERT: E 269 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 287 GLN cc_start: 0.7598 (tp40) cc_final: 0.7157 (tp40) REVERT: E 288 GLU cc_start: 0.7587 (pt0) cc_final: 0.7161 (pt0) REVERT: E 291 ASP cc_start: 0.7431 (p0) cc_final: 0.7070 (p0) REVERT: F 6 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7682 (mtpp) REVERT: F 45 THR cc_start: 0.8563 (m) cc_final: 0.8338 (p) REVERT: F 59 SER cc_start: 0.8719 (m) cc_final: 0.8176 (p) REVERT: F 66 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8112 (mtt90) REVERT: F 69 THR cc_start: 0.8109 (p) cc_final: 0.6999 (m) REVERT: F 72 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: F 97 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7257 (mt-10) REVERT: F 126 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8663 (mptt) REVERT: F 180 THR cc_start: 0.8401 (m) cc_final: 0.8128 (p) REVERT: F 190 GLU cc_start: 0.7693 (mp0) cc_final: 0.7092 (mp0) REVERT: F 209 GLU cc_start: 0.8003 (tt0) cc_final: 0.7678 (tt0) REVERT: F 211 ARG cc_start: 0.8640 (mmt180) cc_final: 0.8325 (mmt180) REVERT: F 215 MET cc_start: 0.8309 (mtm) cc_final: 0.7958 (mtm) REVERT: F 236 THR cc_start: 0.8856 (t) cc_final: 0.8457 (p) REVERT: F 253 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7590 (tm-30) REVERT: F 265 LEU cc_start: 0.8555 (mt) cc_final: 0.8342 (mp) REVERT: F 290 ASN cc_start: 0.8157 (m-40) cc_final: 0.7770 (m-40) REVERT: F 295 ASN cc_start: 0.8209 (m-40) cc_final: 0.7852 (t0) REVERT: F 298 GLU cc_start: 0.8267 (mp0) cc_final: 0.7701 (mp0) REVERT: F 312 ASP cc_start: 0.8454 (t0) cc_final: 0.8247 (m-30) REVERT: G 6 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8346 (ttpt) REVERT: G 8 GLN cc_start: 0.8379 (mt0) cc_final: 0.8134 (mt0) REVERT: G 25 LEU cc_start: 0.8172 (mp) cc_final: 0.7811 (mp) REVERT: G 72 GLU cc_start: 0.7582 (mp0) cc_final: 0.7138 (mp0) REVERT: G 123 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7477 (tm-30) REVERT: G 127 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (t) REVERT: G 162 MET cc_start: -0.1846 (tpp) cc_final: -0.2186 (tpp) REVERT: G 177 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (p) REVERT: G 182 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7937 (mt-10) REVERT: G 183 SER cc_start: 0.8259 (t) cc_final: 0.8024 (p) REVERT: G 188 THR cc_start: 0.8470 (p) cc_final: 0.8185 (p) REVERT: G 194 TYR cc_start: 0.8312 (t80) cc_final: 0.7862 (t80) REVERT: G 216 LYS cc_start: 0.8276 (tppt) cc_final: 0.7825 (tppt) REVERT: G 239 LEU cc_start: 0.8701 (tp) cc_final: 0.8214 (tp) REVERT: G 260 THR cc_start: 0.8408 (t) cc_final: 0.8184 (p) REVERT: G 268 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7517 (mtmt) REVERT: G 288 GLU cc_start: 0.8193 (tp30) cc_final: 0.7573 (tp30) REVERT: G 305 SER cc_start: 0.7961 (m) cc_final: 0.7665 (p) REVERT: H 19 SER cc_start: 0.8657 (p) cc_final: 0.8439 (p) REVERT: H 20 ARG cc_start: 0.8318 (ptp-110) cc_final: 0.8064 (ptp-110) REVERT: H 27 GLU cc_start: 0.7840 (pt0) cc_final: 0.7594 (pt0) REVERT: H 59 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8104 (mm110) REVERT: H 68 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8214 (mtp180) REVERT: H 180 TYR cc_start: 0.8752 (p90) cc_final: 0.8428 (p90) REVERT: H 196 GLN cc_start: 0.8353 (pt0) cc_final: 0.7928 (pt0) REVERT: H 217 GLN cc_start: 0.7949 (tt0) cc_final: 0.7715 (tt0) REVERT: H 228 PHE cc_start: 0.8710 (m-80) cc_final: 0.8437 (m-80) REVERT: I 34 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7589 (mm-30) REVERT: I 84 ASN cc_start: 0.7963 (m-40) cc_final: 0.7436 (m110) REVERT: I 220 ASP cc_start: 0.7756 (m-30) cc_final: 0.7242 (m-30) REVERT: I 241 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7525 (mmmt) REVERT: I 245 TYR cc_start: 0.8075 (p90) cc_final: 0.7863 (p90) REVERT: I 271 ASP cc_start: 0.8146 (m-30) cc_final: 0.7893 (t0) REVERT: I 284 TYR cc_start: 0.7805 (m-80) cc_final: 0.7124 (m-80) REVERT: I 291 GLU cc_start: 0.8015 (pm20) cc_final: 0.7734 (pm20) REVERT: I 298 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8685 (tp) REVERT: I 501 GLN cc_start: 0.8099 (tt0) cc_final: 0.7653 (tt0) REVERT: I 512 GLN cc_start: 0.8012 (tp40) cc_final: 0.7220 (tm-30) REVERT: I 574 SER cc_start: 0.8840 (t) cc_final: 0.8397 (p) REVERT: I 580 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7987 (mtt180) REVERT: I 600 TYR cc_start: 0.8619 (m-80) cc_final: 0.8383 (m-80) REVERT: I 605 TYR cc_start: 0.7811 (m-80) cc_final: 0.7364 (m-80) REVERT: I 619 VAL cc_start: 0.8869 (t) cc_final: 0.8580 (p) REVERT: I 620 TYR cc_start: 0.8149 (m-80) cc_final: 0.6864 (m-80) REVERT: I 638 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8136 (mmmt) REVERT: I 639 MET cc_start: 0.7706 (mmp) cc_final: 0.7465 (mmp) REVERT: I 667 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7301 (mm-30) REVERT: I 668 ASP cc_start: 0.7231 (p0) cc_final: 0.6988 (p0) REVERT: I 684 ASP cc_start: 0.7666 (t70) cc_final: 0.7416 (t70) REVERT: I 705 LYS cc_start: 0.8486 (mttm) cc_final: 0.8239 (mttm) REVERT: I 707 ILE cc_start: 0.8848 (tt) cc_final: 0.8436 (pt) REVERT: I 746 VAL cc_start: 0.8687 (p) cc_final: 0.8458 (p) REVERT: I 749 ILE cc_start: 0.8590 (pt) cc_final: 0.8304 (mm) REVERT: I 767 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7186 (ttm110) REVERT: I 776 GLN cc_start: 0.8168 (mp10) cc_final: 0.7832 (mp10) REVERT: I 783 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7663 (tm-30) REVERT: I 830 MET cc_start: 0.8120 (mtm) cc_final: 0.7784 (mtm) REVERT: I 832 GLU cc_start: 0.8375 (tp30) cc_final: 0.8158 (tp30) REVERT: I 833 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8460 (ttmm) REVERT: I 859 HIS cc_start: 0.8799 (t70) cc_final: 0.8233 (t70) REVERT: I 870 GLU cc_start: 0.7946 (tp30) cc_final: 0.7386 (tp30) REVERT: I 901 VAL cc_start: 0.8802 (t) cc_final: 0.8552 (p) REVERT: I 909 ASP cc_start: 0.7664 (p0) cc_final: 0.7373 (p0) REVERT: I 917 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.8275 (mtm180) REVERT: I 920 GLN cc_start: 0.8391 (mt0) cc_final: 0.8042 (mt0) REVERT: I 923 GLU cc_start: 0.7845 (pp20) cc_final: 0.7636 (pp20) REVERT: I 942 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8874 (mmmt) REVERT: I 963 TYR cc_start: 0.9152 (t80) cc_final: 0.8362 (t80) REVERT: J 5 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4039 (pt) REVERT: J 63 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7862 (tt) REVERT: J 86 GLU cc_start: 0.7612 (pm20) cc_final: 0.7309 (pm20) REVERT: J 88 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7466 (mtm-85) REVERT: J 90 LEU cc_start: 0.8350 (tt) cc_final: 0.8122 (tt) REVERT: J 92 GLU cc_start: 0.8125 (tp30) cc_final: 0.7619 (tp30) REVERT: J 94 GLU cc_start: 0.8133 (pt0) cc_final: 0.7689 (pt0) REVERT: J 110 GLU cc_start: 0.8036 (tp30) cc_final: 0.7363 (tp30) REVERT: J 111 MET cc_start: 0.8242 (ttm) cc_final: 0.8023 (mtp) REVERT: J 120 GLN cc_start: 0.8472 (tp40) cc_final: 0.7957 (tt0) REVERT: J 125 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7863 (mtt90) REVERT: K 13 GLU cc_start: 0.7138 (tt0) cc_final: 0.6881 (tt0) REVERT: K 22 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6094 (pp20) REVERT: K 34 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6800 (tp) REVERT: K 41 GLU cc_start: 0.7239 (tp30) cc_final: 0.6622 (tp30) REVERT: K 52 GLU cc_start: 0.7805 (pp20) cc_final: 0.7303 (pp20) REVERT: K 71 GLU cc_start: 0.7358 (pm20) cc_final: 0.6657 (pm20) REVERT: K 94 GLU cc_start: 0.7823 (tp30) cc_final: 0.7123 (tp30) REVERT: K 131 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7291 (tp30) outliers start: 119 outliers final: 68 residues processed: 1029 average time/residue: 0.2129 time to fit residues: 331.8640 Evaluate side-chains 1029 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 943 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 516 ASN Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 834 LEU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN C 171 HIS ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 99 ASN E 171 HIS E 208 GLN F 68 GLN F 198 ASN F 232 ASN F 263 GLN G 198 ASN G 309 GLN H 95 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 204 HIS I 235 ASN I 257 ASN I 661 GLN I 953 ASN K 20 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113060 restraints weight = 44113.349| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.92 r_work: 0.3312 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29660 Z= 0.260 Angle : 0.704 9.710 40467 Z= 0.367 Chirality : 0.048 0.395 4565 Planarity : 0.005 0.058 4974 Dihedral : 15.573 179.566 4955 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.71 % Allowed : 17.97 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -0.18 (0.14), residues: 3399 helix: 0.69 (0.14), residues: 1498 sheet: -0.11 (0.23), residues: 406 loop : -0.89 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 204 TYR 0.025 0.002 TYR I 844 PHE 0.029 0.002 PHE E 151 TRP 0.043 0.002 TRP I 154 HIS 0.012 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00566 (29660) covalent geometry : angle 0.70361 (40467) hydrogen bonds : bond 0.04216 ( 1334) hydrogen bonds : angle 4.70405 ( 3811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1024 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.8107 (t) cc_final: 0.7723 (p) REVERT: A 78 GLU cc_start: 0.8228 (tt0) cc_final: 0.7975 (tt0) REVERT: A 142 HIS cc_start: 0.8818 (p-80) cc_final: 0.8286 (p-80) REVERT: A 155 THR cc_start: 0.7964 (m) cc_final: 0.7682 (t) REVERT: A 166 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 182 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7832 (mt-10) REVERT: A 210 SER cc_start: 0.8832 (m) cc_final: 0.8626 (m) REVERT: A 228 GLU cc_start: 0.7760 (pt0) cc_final: 0.7523 (pt0) REVERT: A 253 GLU cc_start: 0.8078 (tp30) cc_final: 0.7510 (tp30) REVERT: A 272 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7951 (ttt180) REVERT: A 290 ASN cc_start: 0.8461 (m-40) cc_final: 0.8043 (m-40) REVERT: B 87 SER cc_start: 0.8649 (t) cc_final: 0.8266 (t) REVERT: B 123 GLU cc_start: 0.7833 (tp30) cc_final: 0.7528 (tp30) REVERT: B 128 TYR cc_start: 0.8614 (m-10) cc_final: 0.8241 (m-80) REVERT: B 226 ASP cc_start: 0.7512 (p0) cc_final: 0.6947 (p0) REVERT: B 248 ASN cc_start: 0.8156 (m110) cc_final: 0.7948 (p0) REVERT: B 253 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 256 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 268 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8513 (mtmm) REVERT: B 272 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8109 (mtm180) REVERT: B 287 GLN cc_start: 0.8373 (tp40) cc_final: 0.8147 (tp40) REVERT: B 288 GLU cc_start: 0.8244 (tt0) cc_final: 0.7833 (tt0) REVERT: B 298 GLU cc_start: 0.7994 (tp30) cc_final: 0.7735 (tp30) REVERT: B 308 GLN cc_start: 0.8619 (tp40) cc_final: 0.8330 (tp40) REVERT: C 1 MET cc_start: 0.7989 (tpt) cc_final: 0.7558 (tpt) REVERT: C 5 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 6 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8452 (mtmt) REVERT: C 18 SER cc_start: 0.8440 (m) cc_final: 0.7992 (p) REVERT: C 53 GLU cc_start: 0.7564 (pt0) cc_final: 0.7281 (pt0) REVERT: C 89 ASP cc_start: 0.7908 (m-30) cc_final: 0.7618 (m-30) REVERT: C 90 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8482 (mmmm) REVERT: C 226 ASP cc_start: 0.7870 (t0) cc_final: 0.7662 (t0) REVERT: C 241 ASP cc_start: 0.8474 (t0) cc_final: 0.8258 (t0) REVERT: C 246 GLU cc_start: 0.7965 (pt0) cc_final: 0.7509 (pt0) REVERT: C 249 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: C 264 ASP cc_start: 0.8038 (t70) cc_final: 0.7725 (t0) REVERT: C 268 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8531 (mtmm) REVERT: C 269 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 275 GLU cc_start: 0.7839 (tt0) cc_final: 0.7458 (tt0) REVERT: C 288 GLU cc_start: 0.8146 (tt0) cc_final: 0.7781 (tt0) REVERT: C 302 LEU cc_start: 0.8885 (tp) cc_final: 0.8676 (mp) REVERT: C 303 LEU cc_start: 0.8862 (mt) cc_final: 0.8643 (mp) REVERT: C 316 GLU cc_start: 0.8050 (tp30) cc_final: 0.7780 (tp30) REVERT: D 93 LYS cc_start: 0.8286 (tppt) cc_final: 0.7989 (tppt) REVERT: D 127 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8435 (t) REVERT: D 215 MET cc_start: 0.8304 (mtp) cc_final: 0.7991 (mtt) REVERT: D 243 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8507 (mtp) REVERT: D 253 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 3 ASP cc_start: 0.8229 (p0) cc_final: 0.7954 (p0) REVERT: E 104 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7145 (p) REVERT: E 140 GLN cc_start: 0.8462 (mp10) cc_final: 0.8048 (mp10) REVERT: E 173 LEU cc_start: 0.8535 (mp) cc_final: 0.8232 (mp) REVERT: E 182 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7452 (tm-30) REVERT: E 183 SER cc_start: 0.8381 (t) cc_final: 0.8018 (m) REVERT: E 190 GLU cc_start: 0.7740 (mp0) cc_final: 0.7151 (mp0) REVERT: E 201 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7227 (mtp85) REVERT: E 205 TYR cc_start: 0.7954 (m-80) cc_final: 0.7208 (m-80) REVERT: E 253 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7191 (tm-30) REVERT: E 269 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7424 (mm-30) REVERT: E 287 GLN cc_start: 0.7880 (tp40) cc_final: 0.6738 (tp-100) REVERT: E 288 GLU cc_start: 0.7707 (pt0) cc_final: 0.7298 (pt0) REVERT: E 291 ASP cc_start: 0.7490 (p0) cc_final: 0.6954 (p0) REVERT: F 1 MET cc_start: 0.8555 (tpp) cc_final: 0.8340 (tpp) REVERT: F 18 SER cc_start: 0.8672 (m) cc_final: 0.8082 (p) REVERT: F 59 SER cc_start: 0.8799 (m) cc_final: 0.7996 (p) REVERT: F 66 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8126 (mmt90) REVERT: F 68 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7686 (tp40) REVERT: F 69 THR cc_start: 0.8237 (p) cc_final: 0.6950 (m) REVERT: F 72 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: F 82 ASN cc_start: 0.9085 (t0) cc_final: 0.8672 (t0) REVERT: F 97 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7280 (mt-10) REVERT: F 126 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8590 (mptt) REVERT: F 138 TYR cc_start: 0.8326 (t80) cc_final: 0.7880 (t80) REVERT: F 139 GLU cc_start: 0.7812 (mp0) cc_final: 0.7326 (mp0) REVERT: F 173 LEU cc_start: 0.8585 (tp) cc_final: 0.8336 (tt) REVERT: F 180 THR cc_start: 0.8287 (m) cc_final: 0.7983 (p) REVERT: F 190 GLU cc_start: 0.7692 (mp0) cc_final: 0.7024 (mp0) REVERT: F 211 ARG cc_start: 0.8650 (mmt180) cc_final: 0.8287 (mmt180) REVERT: F 215 MET cc_start: 0.8364 (mtm) cc_final: 0.7871 (mtt) REVERT: F 236 THR cc_start: 0.8870 (t) cc_final: 0.8482 (p) REVERT: G 6 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8385 (ttpt) REVERT: G 8 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: G 43 ASN cc_start: 0.7397 (m110) cc_final: 0.7187 (m110) REVERT: G 48 GLN cc_start: 0.7411 (pt0) cc_final: 0.7064 (pt0) REVERT: G 54 LYS cc_start: 0.6599 (pttm) cc_final: 0.6153 (pttm) REVERT: G 60 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7755 (ptp-170) REVERT: G 72 GLU cc_start: 0.7648 (mp0) cc_final: 0.6964 (mp0) REVERT: G 106 GLN cc_start: 0.8514 (pt0) cc_final: 0.8232 (pt0) REVERT: G 123 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7603 (tm-30) REVERT: G 127 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8153 (t) REVERT: G 128 TYR cc_start: 0.8301 (m-80) cc_final: 0.7924 (m-80) REVERT: G 162 MET cc_start: -0.1759 (tpp) cc_final: -0.2176 (tpp) REVERT: G 177 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7929 (p) REVERT: G 182 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7982 (mt-10) REVERT: G 183 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8041 (p) REVERT: G 194 TYR cc_start: 0.8485 (t80) cc_final: 0.8094 (t80) REVERT: G 198 ASN cc_start: 0.8173 (m-40) cc_final: 0.7896 (t0) REVERT: G 216 LYS cc_start: 0.8268 (tppt) cc_final: 0.7834 (tppt) REVERT: G 240 TYR cc_start: 0.8595 (t80) cc_final: 0.8127 (t80) REVERT: G 260 THR cc_start: 0.8475 (t) cc_final: 0.8272 (p) REVERT: G 267 ASN cc_start: 0.8212 (m-40) cc_final: 0.7907 (m-40) REVERT: G 268 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7504 (mtmt) REVERT: G 272 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7591 (mtm180) REVERT: G 273 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: G 275 GLU cc_start: 0.7911 (tt0) cc_final: 0.7585 (mt-10) REVERT: G 288 GLU cc_start: 0.8170 (tp30) cc_final: 0.7575 (tp30) REVERT: G 295 ASN cc_start: 0.7503 (t0) cc_final: 0.7056 (t0) REVERT: G 307 TYR cc_start: 0.8029 (t80) cc_final: 0.7411 (t80) REVERT: H 19 SER cc_start: 0.8704 (p) cc_final: 0.8495 (p) REVERT: H 38 SER cc_start: 0.8872 (p) cc_final: 0.8517 (m) REVERT: H 39 TYR cc_start: 0.8831 (m-10) cc_final: 0.8488 (m-80) REVERT: H 59 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8198 (mm110) REVERT: H 68 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8503 (mtp180) REVERT: H 227 THR cc_start: 0.8773 (t) cc_final: 0.8567 (t) REVERT: H 228 PHE cc_start: 0.8754 (m-80) cc_final: 0.8379 (m-80) REVERT: I 33 GLU cc_start: 0.7872 (pp20) cc_final: 0.7390 (pp20) REVERT: I 34 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7579 (mm-30) REVERT: I 84 ASN cc_start: 0.7965 (m-40) cc_final: 0.7494 (m110) REVERT: I 220 ASP cc_start: 0.7827 (m-30) cc_final: 0.7269 (m-30) REVERT: I 235 ASN cc_start: 0.8441 (t0) cc_final: 0.8209 (t0) REVERT: I 241 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7429 (mmmt) REVERT: I 271 ASP cc_start: 0.8205 (m-30) cc_final: 0.7950 (t0) REVERT: I 284 TYR cc_start: 0.7821 (m-80) cc_final: 0.7159 (m-80) REVERT: I 291 GLU cc_start: 0.8100 (pm20) cc_final: 0.7866 (pm20) REVERT: I 491 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: I 496 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7378 (ttm110) REVERT: I 512 GLN cc_start: 0.8051 (tp40) cc_final: 0.7657 (tm-30) REVERT: I 574 SER cc_start: 0.8790 (t) cc_final: 0.8261 (p) REVERT: I 600 TYR cc_start: 0.8684 (m-80) cc_final: 0.8440 (m-80) REVERT: I 605 TYR cc_start: 0.7862 (m-80) cc_final: 0.7412 (m-80) REVERT: I 620 TYR cc_start: 0.8284 (m-80) cc_final: 0.7190 (m-80) REVERT: I 638 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8196 (mmmt) REVERT: I 639 MET cc_start: 0.7747 (mmp) cc_final: 0.7453 (mmp) REVERT: I 667 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7405 (mm-30) REVERT: I 668 ASP cc_start: 0.7253 (p0) cc_final: 0.6693 (p0) REVERT: I 696 LEU cc_start: 0.8653 (mt) cc_final: 0.8387 (mm) REVERT: I 724 GLU cc_start: 0.7304 (pm20) cc_final: 0.7018 (pm20) REVERT: I 746 VAL cc_start: 0.8696 (p) cc_final: 0.8464 (p) REVERT: I 749 ILE cc_start: 0.8678 (pt) cc_final: 0.8420 (mm) REVERT: I 754 ASN cc_start: 0.8615 (m-40) cc_final: 0.8325 (m-40) REVERT: I 772 LYS cc_start: 0.7534 (mptp) cc_final: 0.7267 (mptp) REVERT: I 776 GLN cc_start: 0.8186 (mp10) cc_final: 0.7857 (mp10) REVERT: I 783 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7683 (tm-30) REVERT: I 802 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8245 (ttp80) REVERT: I 827 ASN cc_start: 0.8201 (t0) cc_final: 0.7897 (t0) REVERT: I 830 MET cc_start: 0.8061 (mtm) cc_final: 0.7580 (mtm) REVERT: I 832 GLU cc_start: 0.8374 (tp30) cc_final: 0.8162 (tp30) REVERT: I 833 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8520 (ttmm) REVERT: I 870 GLU cc_start: 0.7989 (tp30) cc_final: 0.7438 (tp30) REVERT: I 881 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7764 (pp20) REVERT: I 901 VAL cc_start: 0.8836 (t) cc_final: 0.8605 (p) REVERT: I 902 TYR cc_start: 0.8702 (p90) cc_final: 0.8427 (p90) REVERT: I 909 ASP cc_start: 0.7624 (p0) cc_final: 0.7372 (p0) REVERT: I 910 LYS cc_start: 0.8443 (pttm) cc_final: 0.8184 (pttm) REVERT: I 916 THR cc_start: 0.8322 (p) cc_final: 0.8122 (m) REVERT: I 920 GLN cc_start: 0.8460 (mt0) cc_final: 0.8088 (mt0) REVERT: I 923 GLU cc_start: 0.7909 (pp20) cc_final: 0.7670 (pp20) REVERT: I 940 MET cc_start: 0.8384 (tmm) cc_final: 0.7702 (tmm) REVERT: I 942 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8836 (mmmt) REVERT: I 963 TYR cc_start: 0.9158 (t80) cc_final: 0.8371 (t80) REVERT: J 5 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.4289 (pt) REVERT: J 22 GLU cc_start: 0.7595 (pt0) cc_final: 0.7137 (pt0) REVERT: J 52 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7160 (mm-30) REVERT: J 63 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7966 (tt) REVERT: J 64 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7765 (tm-30) REVERT: J 86 GLU cc_start: 0.7649 (pm20) cc_final: 0.7371 (pm20) REVERT: J 89 GLN cc_start: 0.8311 (mm110) cc_final: 0.8012 (mm-40) REVERT: J 90 LEU cc_start: 0.8408 (tt) cc_final: 0.8138 (tt) REVERT: J 91 GLN cc_start: 0.8545 (mt0) cc_final: 0.8208 (mt0) REVERT: J 92 GLU cc_start: 0.8162 (tp30) cc_final: 0.7776 (tp30) REVERT: J 93 LEU cc_start: 0.8682 (tp) cc_final: 0.8469 (tt) REVERT: J 94 GLU cc_start: 0.8211 (pt0) cc_final: 0.7779 (pt0) REVERT: J 110 GLU cc_start: 0.8101 (tp30) cc_final: 0.7342 (tp30) REVERT: J 111 MET cc_start: 0.8347 (ttm) cc_final: 0.8033 (mtp) REVERT: J 120 GLN cc_start: 0.8438 (tp40) cc_final: 0.8015 (tt0) REVERT: K 13 GLU cc_start: 0.7153 (tt0) cc_final: 0.6890 (tt0) REVERT: K 22 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6058 (pp20) REVERT: K 34 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6797 (tp) REVERT: K 41 GLU cc_start: 0.7269 (tp30) cc_final: 0.6640 (tp30) REVERT: K 44 LEU cc_start: 0.8332 (mt) cc_final: 0.8125 (mp) REVERT: K 52 GLU cc_start: 0.7859 (pp20) cc_final: 0.7337 (pp20) REVERT: K 71 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: K 94 GLU cc_start: 0.7808 (tp30) cc_final: 0.7119 (tp30) REVERT: K 121 GLU cc_start: 0.7131 (tp30) cc_final: 0.6528 (tp30) REVERT: K 131 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7202 (tp30) outliers start: 140 outliers final: 84 residues processed: 1077 average time/residue: 0.2121 time to fit residues: 348.9925 Evaluate side-chains 1099 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 994 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 834 LEU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 131 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 210 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 295 ASN F 43 ASN F 232 ASN G 8 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 95 ASN H 231 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 257 ASN J 20 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114491 restraints weight = 44216.522| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.84 r_work: 0.3328 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29660 Z= 0.191 Angle : 0.656 9.630 40467 Z= 0.342 Chirality : 0.045 0.367 4565 Planarity : 0.004 0.043 4974 Dihedral : 15.493 179.474 4955 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.41 % Allowed : 19.42 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -0.07 (0.14), residues: 3399 helix: 0.88 (0.14), residues: 1503 sheet: -0.20 (0.23), residues: 404 loop : -0.91 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 28 TYR 0.025 0.002 TYR I 245 PHE 0.029 0.001 PHE E 151 TRP 0.045 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00417 (29660) covalent geometry : angle 0.65560 (40467) hydrogen bonds : bond 0.03838 ( 1334) hydrogen bonds : angle 4.58912 ( 3811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1018 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8594 (mm-40) REVERT: A 32 SER cc_start: 0.8140 (t) cc_final: 0.7777 (p) REVERT: A 57 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 78 GLU cc_start: 0.8226 (tt0) cc_final: 0.7973 (tt0) REVERT: A 142 HIS cc_start: 0.8810 (p-80) cc_final: 0.8152 (p-80) REVERT: A 155 THR cc_start: 0.8093 (m) cc_final: 0.7790 (t) REVERT: A 166 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 180 THR cc_start: 0.8307 (p) cc_final: 0.8042 (t) REVERT: A 209 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 228 GLU cc_start: 0.7730 (pt0) cc_final: 0.7441 (pt0) REVERT: A 253 GLU cc_start: 0.8070 (tp30) cc_final: 0.7525 (tp30) REVERT: A 272 ARG cc_start: 0.8159 (tpt170) cc_final: 0.7931 (ttt180) REVERT: A 290 ASN cc_start: 0.8469 (m-40) cc_final: 0.8072 (m-40) REVERT: A 296 ASP cc_start: 0.8071 (t0) cc_final: 0.7848 (t0) REVERT: A 308 GLN cc_start: 0.8225 (tp40) cc_final: 0.7858 (tp-100) REVERT: B 87 SER cc_start: 0.8693 (t) cc_final: 0.8336 (t) REVERT: B 109 ASP cc_start: 0.7988 (t0) cc_final: 0.7728 (t0) REVERT: B 123 GLU cc_start: 0.7783 (tp30) cc_final: 0.7492 (tp30) REVERT: B 190 GLU cc_start: 0.8214 (mp0) cc_final: 0.7738 (mp0) REVERT: B 226 ASP cc_start: 0.7548 (p0) cc_final: 0.7071 (p0) REVERT: B 248 ASN cc_start: 0.8189 (m110) cc_final: 0.7961 (p0) REVERT: B 253 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 256 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 268 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8487 (mtmm) REVERT: B 272 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8374 (mtm180) REVERT: B 287 GLN cc_start: 0.8350 (tp40) cc_final: 0.8076 (tp-100) REVERT: B 288 GLU cc_start: 0.8206 (tt0) cc_final: 0.7884 (tt0) REVERT: B 298 GLU cc_start: 0.7935 (tp30) cc_final: 0.7535 (tp30) REVERT: B 301 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8272 (ttpt) REVERT: B 308 GLN cc_start: 0.8584 (tp40) cc_final: 0.8265 (tp40) REVERT: C 1 MET cc_start: 0.8027 (tpt) cc_final: 0.7585 (tpt) REVERT: C 5 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 6 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8402 (mtmt) REVERT: C 18 SER cc_start: 0.8456 (m) cc_final: 0.8036 (p) REVERT: C 53 GLU cc_start: 0.7488 (pt0) cc_final: 0.7222 (pt0) REVERT: C 109 ASP cc_start: 0.8319 (t70) cc_final: 0.8054 (t0) REVERT: C 241 ASP cc_start: 0.8466 (t0) cc_final: 0.8252 (t0) REVERT: C 246 GLU cc_start: 0.7969 (pt0) cc_final: 0.7460 (pt0) REVERT: C 249 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8587 (mtmm) REVERT: C 264 ASP cc_start: 0.8049 (t70) cc_final: 0.7776 (t0) REVERT: C 268 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8620 (mtmm) REVERT: C 275 GLU cc_start: 0.7831 (tt0) cc_final: 0.7478 (tt0) REVERT: C 288 GLU cc_start: 0.8112 (tt0) cc_final: 0.7848 (tt0) REVERT: C 302 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8660 (mp) REVERT: C 316 GLU cc_start: 0.8075 (tp30) cc_final: 0.7788 (tp30) REVERT: D 62 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8650 (p) REVERT: D 93 LYS cc_start: 0.8249 (tppt) cc_final: 0.7952 (tppt) REVERT: D 190 GLU cc_start: 0.8063 (mp0) cc_final: 0.7555 (mp0) REVERT: D 215 MET cc_start: 0.8276 (mtp) cc_final: 0.8000 (mtt) REVERT: D 243 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: D 253 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7097 (tm-30) REVERT: D 269 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7687 (mm-30) REVERT: E 3 ASP cc_start: 0.8177 (p0) cc_final: 0.7922 (p0) REVERT: E 46 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7945 (mtp85) REVERT: E 104 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7202 (p) REVERT: E 140 GLN cc_start: 0.8425 (mp10) cc_final: 0.8004 (mp10) REVERT: E 173 LEU cc_start: 0.8548 (mp) cc_final: 0.8251 (mp) REVERT: E 182 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7469 (tm-30) REVERT: E 183 SER cc_start: 0.8371 (t) cc_final: 0.7978 (m) REVERT: E 186 ASP cc_start: 0.7321 (p0) cc_final: 0.7083 (p0) REVERT: E 190 GLU cc_start: 0.7646 (mp0) cc_final: 0.7181 (mp0) REVERT: E 201 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: E 205 TYR cc_start: 0.7915 (m-80) cc_final: 0.7264 (m-80) REVERT: E 249 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7559 (mmpt) REVERT: E 253 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7194 (tm-30) REVERT: E 269 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7355 (mm-30) REVERT: E 287 GLN cc_start: 0.7495 (tp40) cc_final: 0.7010 (tp40) REVERT: E 288 GLU cc_start: 0.7644 (pt0) cc_final: 0.7162 (pt0) REVERT: E 291 ASP cc_start: 0.7284 (p0) cc_final: 0.6834 (p0) REVERT: F 6 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7623 (mtpp) REVERT: F 18 SER cc_start: 0.8649 (m) cc_final: 0.8022 (p) REVERT: F 45 THR cc_start: 0.8598 (m) cc_final: 0.8393 (p) REVERT: F 59 SER cc_start: 0.8786 (m) cc_final: 0.7945 (p) REVERT: F 66 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8132 (mpt180) REVERT: F 69 THR cc_start: 0.8190 (p) cc_final: 0.6686 (m) REVERT: F 72 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: F 97 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7249 (mt-10) REVERT: F 138 TYR cc_start: 0.8286 (t80) cc_final: 0.7982 (t80) REVERT: F 139 GLU cc_start: 0.7809 (mp0) cc_final: 0.7294 (mp0) REVERT: F 173 LEU cc_start: 0.8546 (tp) cc_final: 0.8276 (tt) REVERT: F 180 THR cc_start: 0.8245 (m) cc_final: 0.7960 (p) REVERT: F 190 GLU cc_start: 0.7699 (mp0) cc_final: 0.7057 (mp0) REVERT: F 204 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7920 (mtp85) REVERT: F 209 GLU cc_start: 0.7962 (tt0) cc_final: 0.7672 (tt0) REVERT: F 215 MET cc_start: 0.8361 (mtm) cc_final: 0.7911 (mtt) REVERT: F 236 THR cc_start: 0.8871 (t) cc_final: 0.8494 (p) REVERT: F 249 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8005 (mtmt) REVERT: F 295 ASN cc_start: 0.8343 (t0) cc_final: 0.8102 (t0) REVERT: G 6 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8386 (ttpt) REVERT: G 8 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: G 22 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8246 (m) REVERT: G 43 ASN cc_start: 0.7392 (m110) cc_final: 0.7189 (m110) REVERT: G 48 GLN cc_start: 0.7433 (pt0) cc_final: 0.7015 (pt0) REVERT: G 54 LYS cc_start: 0.6665 (pttm) cc_final: 0.6230 (pttm) REVERT: G 72 GLU cc_start: 0.7600 (mp0) cc_final: 0.7192 (mp0) REVERT: G 123 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7456 (tm-30) REVERT: G 128 TYR cc_start: 0.8307 (m-80) cc_final: 0.7894 (m-80) REVERT: G 162 MET cc_start: -0.1780 (tpp) cc_final: -0.2251 (tpp) REVERT: G 177 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7832 (p) REVERT: G 182 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7899 (mt-10) REVERT: G 183 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.8006 (p) REVERT: G 194 TYR cc_start: 0.8487 (t80) cc_final: 0.8109 (t80) REVERT: G 216 LYS cc_start: 0.8278 (tppt) cc_final: 0.7822 (tppt) REVERT: G 240 TYR cc_start: 0.8582 (t80) cc_final: 0.8177 (t80) REVERT: G 260 THR cc_start: 0.8413 (t) cc_final: 0.8203 (p) REVERT: G 267 ASN cc_start: 0.8275 (m-40) cc_final: 0.8015 (m-40) REVERT: G 268 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7533 (mtmt) REVERT: G 272 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7785 (mtm180) REVERT: G 275 GLU cc_start: 0.7853 (tt0) cc_final: 0.7542 (mt-10) REVERT: G 288 GLU cc_start: 0.8110 (tp30) cc_final: 0.7499 (tp30) REVERT: G 295 ASN cc_start: 0.7447 (t0) cc_final: 0.7015 (t0) REVERT: G 307 TYR cc_start: 0.8019 (t80) cc_final: 0.7438 (t80) REVERT: H 13 ASP cc_start: 0.7599 (p0) cc_final: 0.7370 (p0) REVERT: H 38 SER cc_start: 0.8858 (p) cc_final: 0.8506 (m) REVERT: H 39 TYR cc_start: 0.8835 (m-80) cc_final: 0.8412 (m-80) REVERT: H 59 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8128 (mm-40) REVERT: I 33 GLU cc_start: 0.7873 (pp20) cc_final: 0.7446 (pp20) REVERT: I 34 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7632 (mm-30) REVERT: I 84 ASN cc_start: 0.7957 (m-40) cc_final: 0.7483 (m110) REVERT: I 158 ARG cc_start: 0.7307 (ttp80) cc_final: 0.6985 (ttp80) REVERT: I 220 ASP cc_start: 0.7809 (m-30) cc_final: 0.7247 (m-30) REVERT: I 235 ASN cc_start: 0.8448 (t0) cc_final: 0.8181 (t0) REVERT: I 271 ASP cc_start: 0.8140 (m-30) cc_final: 0.7878 (t0) REVERT: I 284 TYR cc_start: 0.7782 (m-80) cc_final: 0.7051 (m-80) REVERT: I 291 GLU cc_start: 0.8073 (pm20) cc_final: 0.7861 (pm20) REVERT: I 493 TYR cc_start: 0.8405 (t80) cc_final: 0.8201 (t80) REVERT: I 501 GLN cc_start: 0.7873 (tt0) cc_final: 0.7600 (tt0) REVERT: I 512 GLN cc_start: 0.8002 (tp40) cc_final: 0.7618 (tm-30) REVERT: I 574 SER cc_start: 0.8722 (t) cc_final: 0.8184 (p) REVERT: I 600 TYR cc_start: 0.8656 (m-80) cc_final: 0.8428 (m-80) REVERT: I 605 TYR cc_start: 0.7816 (m-80) cc_final: 0.7395 (m-80) REVERT: I 620 TYR cc_start: 0.8166 (m-80) cc_final: 0.7280 (m-80) REVERT: I 638 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8136 (mmmt) REVERT: I 639 MET cc_start: 0.7677 (mmp) cc_final: 0.7395 (mmp) REVERT: I 668 ASP cc_start: 0.7166 (p0) cc_final: 0.6888 (p0) REVERT: I 696 LEU cc_start: 0.8613 (mt) cc_final: 0.8367 (mm) REVERT: I 715 LEU cc_start: 0.4625 (tp) cc_final: 0.4329 (tt) REVERT: I 724 GLU cc_start: 0.7338 (pm20) cc_final: 0.7098 (pm20) REVERT: I 746 VAL cc_start: 0.8682 (p) cc_final: 0.8436 (p) REVERT: I 749 ILE cc_start: 0.8627 (pt) cc_final: 0.8401 (mm) REVERT: I 754 ASN cc_start: 0.8637 (m-40) cc_final: 0.8342 (m-40) REVERT: I 772 LYS cc_start: 0.7604 (mptp) cc_final: 0.7286 (mptp) REVERT: I 776 GLN cc_start: 0.8131 (mp10) cc_final: 0.7708 (mp10) REVERT: I 783 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7659 (tm-30) REVERT: I 802 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8279 (ttp80) REVERT: I 827 ASN cc_start: 0.8133 (t0) cc_final: 0.7664 (t0) REVERT: I 830 MET cc_start: 0.8067 (mtm) cc_final: 0.7641 (mtm) REVERT: I 832 GLU cc_start: 0.8277 (tp30) cc_final: 0.8074 (tp30) REVERT: I 870 GLU cc_start: 0.7941 (tp30) cc_final: 0.7387 (tp30) REVERT: I 901 VAL cc_start: 0.8834 (t) cc_final: 0.8595 (p) REVERT: I 902 TYR cc_start: 0.8696 (p90) cc_final: 0.8454 (p90) REVERT: I 909 ASP cc_start: 0.7616 (p0) cc_final: 0.7398 (p0) REVERT: I 910 LYS cc_start: 0.8407 (pttm) cc_final: 0.8158 (pttm) REVERT: I 916 THR cc_start: 0.8273 (p) cc_final: 0.8065 (m) REVERT: I 920 GLN cc_start: 0.8429 (mt0) cc_final: 0.8069 (mt0) REVERT: I 923 GLU cc_start: 0.7883 (pp20) cc_final: 0.7633 (pp20) REVERT: I 942 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8864 (mmmt) REVERT: I 963 TYR cc_start: 0.9106 (t80) cc_final: 0.8276 (t80) REVERT: J 5 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.4449 (pt) REVERT: J 22 GLU cc_start: 0.7581 (pt0) cc_final: 0.7245 (pt0) REVERT: J 63 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (tt) REVERT: J 64 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7825 (tm-30) REVERT: J 73 TYR cc_start: 0.7468 (t80) cc_final: 0.7184 (t80) REVERT: J 88 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7653 (mtt180) REVERT: J 89 GLN cc_start: 0.8300 (mm110) cc_final: 0.8018 (mm110) REVERT: J 90 LEU cc_start: 0.8461 (tt) cc_final: 0.8185 (tt) REVERT: J 91 GLN cc_start: 0.8541 (mt0) cc_final: 0.8240 (mt0) REVERT: J 92 GLU cc_start: 0.8160 (tp30) cc_final: 0.7658 (tp30) REVERT: J 93 LEU cc_start: 0.8707 (tp) cc_final: 0.8482 (tt) REVERT: J 94 GLU cc_start: 0.8138 (pt0) cc_final: 0.7748 (pt0) REVERT: J 110 GLU cc_start: 0.8056 (tp30) cc_final: 0.7389 (tp30) REVERT: J 120 GLN cc_start: 0.8420 (tp40) cc_final: 0.8027 (tt0) REVERT: J 140 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7209 (tm-30) REVERT: K 13 GLU cc_start: 0.7122 (tt0) cc_final: 0.6862 (tt0) REVERT: K 22 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6073 (pp20) REVERT: K 34 LEU cc_start: 0.7008 (tp) cc_final: 0.6778 (tp) REVERT: K 41 GLU cc_start: 0.7267 (tp30) cc_final: 0.6643 (tp30) REVERT: K 44 LEU cc_start: 0.8296 (mt) cc_final: 0.8087 (mp) REVERT: K 52 GLU cc_start: 0.7911 (pp20) cc_final: 0.7302 (pp20) REVERT: K 71 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: K 94 GLU cc_start: 0.7773 (tp30) cc_final: 0.7093 (tp30) REVERT: K 131 GLU cc_start: 0.7526 (tp30) cc_final: 0.7114 (tp30) outliers start: 131 outliers final: 84 residues processed: 1066 average time/residue: 0.2057 time to fit residues: 335.0842 Evaluate side-chains 1086 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 983 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 834 LEU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 126 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 322 optimal weight: 0.0980 chunk 219 optimal weight: 0.0170 chunk 326 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 294 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 241 optimal weight: 0.4980 chunk 189 optimal weight: 0.7980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 68 GLN D 99 ASN D 295 ASN E 198 ASN E 295 ASN F 232 ASN G 198 ASN H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 257 ASN J 58 GLN K 30 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115227 restraints weight = 43826.617| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.86 r_work: 0.3346 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29660 Z= 0.144 Angle : 0.630 9.446 40467 Z= 0.327 Chirality : 0.043 0.365 4565 Planarity : 0.004 0.044 4974 Dihedral : 15.402 179.055 4951 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.51 % Allowed : 19.93 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.04 (0.14), residues: 3399 helix: 1.02 (0.14), residues: 1512 sheet: -0.07 (0.24), residues: 389 loop : -0.95 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 28 TYR 0.023 0.001 TYR I 844 PHE 0.030 0.001 PHE E 151 TRP 0.038 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00311 (29660) covalent geometry : angle 0.62990 (40467) hydrogen bonds : bond 0.03575 ( 1334) hydrogen bonds : angle 4.47123 ( 3811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 987 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8594 (mt0) REVERT: A 32 SER cc_start: 0.8134 (t) cc_final: 0.7764 (p) REVERT: A 57 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7890 (mm-40) REVERT: A 78 GLU cc_start: 0.8245 (tt0) cc_final: 0.8007 (tt0) REVERT: A 138 TYR cc_start: 0.8592 (t80) cc_final: 0.7401 (t80) REVERT: A 142 HIS cc_start: 0.8644 (p-80) cc_final: 0.7718 (p-80) REVERT: A 155 THR cc_start: 0.8058 (m) cc_final: 0.7812 (t) REVERT: A 180 THR cc_start: 0.8310 (p) cc_final: 0.8047 (t) REVERT: A 253 GLU cc_start: 0.8044 (tp30) cc_final: 0.7496 (tp30) REVERT: A 272 ARG cc_start: 0.8108 (tpt170) cc_final: 0.7879 (ttt180) REVERT: A 296 ASP cc_start: 0.8085 (t0) cc_final: 0.7852 (t0) REVERT: A 298 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: A 308 GLN cc_start: 0.8247 (tp40) cc_final: 0.7855 (tp-100) REVERT: B 109 ASP cc_start: 0.7945 (t0) cc_final: 0.7634 (t0) REVERT: B 123 GLU cc_start: 0.7781 (tp30) cc_final: 0.7542 (tp30) REVERT: B 126 LYS cc_start: 0.8744 (mttp) cc_final: 0.8418 (mmtm) REVERT: B 226 ASP cc_start: 0.7528 (p0) cc_final: 0.7040 (p0) REVERT: B 248 ASN cc_start: 0.8151 (m110) cc_final: 0.7932 (p0) REVERT: B 253 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 256 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 268 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8516 (mtmm) REVERT: B 287 GLN cc_start: 0.8332 (tp40) cc_final: 0.8084 (tp40) REVERT: B 288 GLU cc_start: 0.8227 (tt0) cc_final: 0.7886 (tt0) REVERT: B 298 GLU cc_start: 0.7912 (tp30) cc_final: 0.7645 (tp30) REVERT: B 308 GLN cc_start: 0.8585 (tp40) cc_final: 0.8288 (tp40) REVERT: C 1 MET cc_start: 0.8054 (tpt) cc_final: 0.7592 (tpt) REVERT: C 5 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8241 (mt) REVERT: C 6 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8113 (mtmm) REVERT: C 18 SER cc_start: 0.8448 (m) cc_final: 0.8040 (p) REVERT: C 32 SER cc_start: 0.8090 (m) cc_final: 0.7886 (p) REVERT: C 53 GLU cc_start: 0.7440 (pt0) cc_final: 0.7159 (pt0) REVERT: C 109 ASP cc_start: 0.8278 (t70) cc_final: 0.8020 (t0) REVERT: C 203 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8698 (mmmt) REVERT: C 241 ASP cc_start: 0.8480 (t0) cc_final: 0.8275 (t0) REVERT: C 246 GLU cc_start: 0.7946 (pt0) cc_final: 0.7419 (pt0) REVERT: C 249 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: C 264 ASP cc_start: 0.8075 (t70) cc_final: 0.7531 (t0) REVERT: C 268 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8316 (mttm) REVERT: C 275 GLU cc_start: 0.7814 (tt0) cc_final: 0.7470 (tt0) REVERT: C 288 GLU cc_start: 0.8081 (tt0) cc_final: 0.7813 (tt0) REVERT: C 316 GLU cc_start: 0.8100 (tp30) cc_final: 0.7815 (tp30) REVERT: D 62 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 93 LYS cc_start: 0.8213 (tppt) cc_final: 0.7934 (tppt) REVERT: D 130 ASP cc_start: 0.7485 (t0) cc_final: 0.7280 (t0) REVERT: D 215 MET cc_start: 0.8295 (mtp) cc_final: 0.8024 (mtt) REVERT: D 243 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (mtp) REVERT: D 253 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 256 GLU cc_start: 0.8104 (tt0) cc_final: 0.7858 (tt0) REVERT: D 269 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7776 (mm-30) REVERT: E 1 MET cc_start: 0.7843 (ttm) cc_final: 0.7607 (ttt) REVERT: E 3 ASP cc_start: 0.8208 (p0) cc_final: 0.7972 (p0) REVERT: E 46 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.7993 (mtp85) REVERT: E 48 GLN cc_start: 0.7764 (tt0) cc_final: 0.7505 (mt0) REVERT: E 104 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7180 (p) REVERT: E 140 GLN cc_start: 0.8405 (mp10) cc_final: 0.7968 (mp10) REVERT: E 173 LEU cc_start: 0.8508 (mp) cc_final: 0.8203 (mp) REVERT: E 182 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7463 (tm-30) REVERT: E 183 SER cc_start: 0.8378 (t) cc_final: 0.8083 (m) REVERT: E 190 GLU cc_start: 0.7611 (mp0) cc_final: 0.7198 (mp0) REVERT: E 201 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7537 (mtp85) REVERT: E 205 TYR cc_start: 0.7894 (m-80) cc_final: 0.7254 (m-80) REVERT: E 249 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7669 (mmpt) REVERT: E 253 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7103 (tm-30) REVERT: E 269 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 287 GLN cc_start: 0.7487 (tp40) cc_final: 0.7057 (tp40) REVERT: E 288 GLU cc_start: 0.7595 (pt0) cc_final: 0.7150 (pt0) REVERT: E 290 ASN cc_start: 0.7578 (p0) cc_final: 0.7326 (p0) REVERT: E 291 ASP cc_start: 0.7256 (p0) cc_final: 0.6778 (p0) REVERT: F 1 MET cc_start: 0.8453 (tpp) cc_final: 0.8105 (tpp) REVERT: F 6 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7602 (mtpp) REVERT: F 18 SER cc_start: 0.8603 (m) cc_final: 0.7971 (p) REVERT: F 59 SER cc_start: 0.8785 (m) cc_final: 0.7954 (p) REVERT: F 69 THR cc_start: 0.8247 (p) cc_final: 0.7032 (m) REVERT: F 82 ASN cc_start: 0.9026 (t0) cc_final: 0.8806 (t0) REVERT: F 97 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7208 (mt-10) REVERT: F 138 TYR cc_start: 0.8269 (t80) cc_final: 0.7957 (t80) REVERT: F 139 GLU cc_start: 0.7769 (mp0) cc_final: 0.7257 (mp0) REVERT: F 173 LEU cc_start: 0.8534 (tp) cc_final: 0.8262 (tt) REVERT: F 180 THR cc_start: 0.8216 (m) cc_final: 0.7955 (p) REVERT: F 190 GLU cc_start: 0.7695 (mp0) cc_final: 0.7081 (mp0) REVERT: F 209 GLU cc_start: 0.7971 (tt0) cc_final: 0.7602 (tt0) REVERT: F 236 THR cc_start: 0.8871 (t) cc_final: 0.8504 (p) REVERT: F 249 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7981 (mtmt) REVERT: F 265 LEU cc_start: 0.8528 (mt) cc_final: 0.8315 (mp) REVERT: F 295 ASN cc_start: 0.8336 (t0) cc_final: 0.8070 (t0) REVERT: G 6 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8304 (ttpt) REVERT: G 8 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: G 22 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8223 (m) REVERT: G 48 GLN cc_start: 0.7409 (pt0) cc_final: 0.6976 (pt0) REVERT: G 54 LYS cc_start: 0.6669 (pttm) cc_final: 0.6215 (pttm) REVERT: G 72 GLU cc_start: 0.7679 (mp0) cc_final: 0.7035 (mp0) REVERT: G 128 TYR cc_start: 0.8243 (m-80) cc_final: 0.7802 (m-80) REVERT: G 162 MET cc_start: -0.1867 (tpp) cc_final: -0.2398 (tpp) REVERT: G 177 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7819 (p) REVERT: G 181 VAL cc_start: 0.8731 (t) cc_final: 0.8333 (p) REVERT: G 182 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7839 (mt-10) REVERT: G 183 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7999 (p) REVERT: G 194 TYR cc_start: 0.8475 (t80) cc_final: 0.8111 (t80) REVERT: G 198 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7862 (t0) REVERT: G 216 LYS cc_start: 0.8222 (tppt) cc_final: 0.7828 (tppt) REVERT: G 240 TYR cc_start: 0.8555 (t80) cc_final: 0.8161 (t80) REVERT: G 260 THR cc_start: 0.8410 (t) cc_final: 0.8192 (p) REVERT: G 267 ASN cc_start: 0.8313 (m-40) cc_final: 0.8084 (m-40) REVERT: G 268 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7556 (mtmt) REVERT: G 272 ARG cc_start: 0.8207 (mtm180) cc_final: 0.7591 (mtm180) REVERT: G 288 GLU cc_start: 0.8136 (tp30) cc_final: 0.7668 (tp30) REVERT: G 295 ASN cc_start: 0.7418 (t0) cc_final: 0.6945 (t0) REVERT: H 13 ASP cc_start: 0.7649 (p0) cc_final: 0.7443 (p0) REVERT: H 39 TYR cc_start: 0.8835 (m-80) cc_final: 0.8422 (m-80) REVERT: H 59 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8079 (mm110) REVERT: H 180 TYR cc_start: 0.8814 (p90) cc_final: 0.8381 (p90) REVERT: H 199 LEU cc_start: 0.8198 (mt) cc_final: 0.7860 (mp) REVERT: H 209 SER cc_start: 0.8538 (p) cc_final: 0.8330 (m) REVERT: I 33 GLU cc_start: 0.7826 (pp20) cc_final: 0.7427 (pp20) REVERT: I 84 ASN cc_start: 0.7937 (m-40) cc_final: 0.7467 (m110) REVERT: I 158 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6930 (ttp80) REVERT: I 189 TYR cc_start: 0.8253 (m-80) cc_final: 0.8052 (m-80) REVERT: I 220 ASP cc_start: 0.7822 (m-30) cc_final: 0.7159 (m-30) REVERT: I 235 ASN cc_start: 0.8461 (t0) cc_final: 0.8233 (t0) REVERT: I 271 ASP cc_start: 0.8128 (m-30) cc_final: 0.7866 (t0) REVERT: I 284 TYR cc_start: 0.7708 (m-80) cc_final: 0.6911 (m-80) REVERT: I 291 GLU cc_start: 0.8073 (pm20) cc_final: 0.7869 (pm20) REVERT: I 491 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: I 496 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7644 (ttm170) REVERT: I 512 GLN cc_start: 0.7964 (tp40) cc_final: 0.7603 (tm-30) REVERT: I 574 SER cc_start: 0.8641 (t) cc_final: 0.8090 (p) REVERT: I 600 TYR cc_start: 0.8640 (m-80) cc_final: 0.8410 (m-80) REVERT: I 605 TYR cc_start: 0.7801 (m-80) cc_final: 0.7421 (m-80) REVERT: I 620 TYR cc_start: 0.8142 (m-80) cc_final: 0.7245 (m-80) REVERT: I 639 MET cc_start: 0.7626 (mmp) cc_final: 0.7398 (mmp) REVERT: I 668 ASP cc_start: 0.7113 (p0) cc_final: 0.6836 (p0) REVERT: I 696 LEU cc_start: 0.8592 (mt) cc_final: 0.8368 (mm) REVERT: I 715 LEU cc_start: 0.4492 (tp) cc_final: 0.3876 (tt) REVERT: I 724 GLU cc_start: 0.7368 (pm20) cc_final: 0.7153 (pm20) REVERT: I 746 VAL cc_start: 0.8656 (p) cc_final: 0.8411 (p) REVERT: I 750 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8644 (m) REVERT: I 754 ASN cc_start: 0.8624 (m-40) cc_final: 0.8316 (m-40) REVERT: I 772 LYS cc_start: 0.7514 (mptp) cc_final: 0.7182 (mptp) REVERT: I 776 GLN cc_start: 0.8104 (mp10) cc_final: 0.7702 (mp10) REVERT: I 783 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7654 (tm-30) REVERT: I 802 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8289 (ttp80) REVERT: I 827 ASN cc_start: 0.8076 (t0) cc_final: 0.7800 (t0) REVERT: I 830 MET cc_start: 0.8058 (mtm) cc_final: 0.7732 (mtm) REVERT: I 832 GLU cc_start: 0.8279 (tp30) cc_final: 0.8075 (tp30) REVERT: I 833 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8339 (ttmm) REVERT: I 870 GLU cc_start: 0.7848 (tp30) cc_final: 0.7269 (tp30) REVERT: I 881 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7682 (pp20) REVERT: I 901 VAL cc_start: 0.8824 (t) cc_final: 0.8587 (p) REVERT: I 902 TYR cc_start: 0.8706 (p90) cc_final: 0.8469 (p90) REVERT: I 910 LYS cc_start: 0.8409 (pttm) cc_final: 0.8158 (pttm) REVERT: I 916 THR cc_start: 0.8237 (p) cc_final: 0.8028 (m) REVERT: I 920 GLN cc_start: 0.8438 (mt0) cc_final: 0.8068 (mt0) REVERT: I 923 GLU cc_start: 0.7873 (pp20) cc_final: 0.7594 (pp20) REVERT: I 942 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8867 (mmmt) REVERT: I 963 TYR cc_start: 0.9100 (t80) cc_final: 0.8220 (t80) REVERT: J 5 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4181 (pt) REVERT: J 22 GLU cc_start: 0.7600 (pt0) cc_final: 0.7324 (pt0) REVERT: J 52 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6832 (mm-30) REVERT: J 58 GLN cc_start: 0.8271 (mt0) cc_final: 0.8044 (mt0) REVERT: J 63 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8297 (tp) REVERT: J 64 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8128 (tm-30) REVERT: J 67 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7679 (mt) REVERT: J 73 TYR cc_start: 0.7397 (t80) cc_final: 0.7143 (t80) REVERT: J 88 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7634 (mtt180) REVERT: J 89 GLN cc_start: 0.8289 (mm110) cc_final: 0.8008 (mm110) REVERT: J 90 LEU cc_start: 0.8423 (tt) cc_final: 0.8134 (tt) REVERT: J 91 GLN cc_start: 0.8535 (mt0) cc_final: 0.8227 (mt0) REVERT: J 92 GLU cc_start: 0.8149 (tp30) cc_final: 0.7678 (tp30) REVERT: J 93 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (tt) REVERT: J 94 GLU cc_start: 0.8178 (pt0) cc_final: 0.7741 (pt0) REVERT: J 110 GLU cc_start: 0.8025 (tp30) cc_final: 0.7294 (tp30) REVERT: J 120 GLN cc_start: 0.8386 (tp40) cc_final: 0.8016 (tt0) REVERT: J 125 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7554 (mtt90) REVERT: J 140 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7215 (tm-30) REVERT: J 143 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7334 (tp40) REVERT: K 13 GLU cc_start: 0.7110 (tt0) cc_final: 0.6843 (tt0) REVERT: K 22 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6051 (pp20) REVERT: K 41 GLU cc_start: 0.7210 (tp30) cc_final: 0.6582 (tp30) REVERT: K 52 GLU cc_start: 0.7909 (pp20) cc_final: 0.7308 (pp20) REVERT: K 71 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6516 (pm20) REVERT: K 94 GLU cc_start: 0.7756 (tp30) cc_final: 0.7098 (tp30) REVERT: K 131 GLU cc_start: 0.7531 (tp30) cc_final: 0.7091 (tp30) outliers start: 134 outliers final: 75 residues processed: 1037 average time/residue: 0.2078 time to fit residues: 328.9094 Evaluate side-chains 1073 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 976 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 149 optimal weight: 0.8980 chunk 346 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 266 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN C 20 HIS ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN E 31 GLN E 295 ASN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 140 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114067 restraints weight = 43978.373| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.92 r_work: 0.3327 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29660 Z= 0.183 Angle : 0.651 12.619 40467 Z= 0.336 Chirality : 0.045 0.360 4565 Planarity : 0.004 0.044 4974 Dihedral : 15.313 179.407 4940 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.44 % Allowed : 20.77 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.12 (0.14), residues: 3399 helix: 1.14 (0.14), residues: 1482 sheet: -0.17 (0.23), residues: 409 loop : -0.89 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 272 TYR 0.024 0.002 TYR I 245 PHE 0.031 0.002 PHE E 151 TRP 0.035 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00401 (29660) covalent geometry : angle 0.65150 (40467) hydrogen bonds : bond 0.03655 ( 1334) hydrogen bonds : angle 4.47079 ( 3811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 970 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8614 (mt0) REVERT: A 32 SER cc_start: 0.8167 (t) cc_final: 0.7793 (p) REVERT: A 57 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 78 GLU cc_start: 0.8257 (tt0) cc_final: 0.8034 (tt0) REVERT: A 138 TYR cc_start: 0.8627 (t80) cc_final: 0.7498 (t80) REVERT: A 142 HIS cc_start: 0.8731 (p-80) cc_final: 0.7896 (p-80) REVERT: A 155 THR cc_start: 0.8096 (m) cc_final: 0.7842 (t) REVERT: A 180 THR cc_start: 0.8318 (p) cc_final: 0.8068 (t) REVERT: A 253 GLU cc_start: 0.8056 (tp30) cc_final: 0.7503 (tp30) REVERT: A 272 ARG cc_start: 0.8154 (tpt170) cc_final: 0.7924 (ttt180) REVERT: A 290 ASN cc_start: 0.8592 (m-40) cc_final: 0.8158 (m-40) REVERT: A 296 ASP cc_start: 0.8120 (t0) cc_final: 0.7892 (t0) REVERT: A 298 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: A 308 GLN cc_start: 0.8246 (tp40) cc_final: 0.7852 (tp-100) REVERT: B 109 ASP cc_start: 0.8051 (t0) cc_final: 0.7731 (t0) REVERT: B 123 GLU cc_start: 0.7823 (tp30) cc_final: 0.7604 (tp30) REVERT: B 162 MET cc_start: 0.8534 (mmt) cc_final: 0.8190 (mmm) REVERT: B 190 GLU cc_start: 0.8041 (mp0) cc_final: 0.7819 (mp0) REVERT: B 248 ASN cc_start: 0.8268 (m110) cc_final: 0.8012 (p0) REVERT: B 253 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 256 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 268 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8541 (mtmm) REVERT: B 272 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8273 (mtm180) REVERT: B 287 GLN cc_start: 0.8371 (tp40) cc_final: 0.8135 (tp40) REVERT: B 288 GLU cc_start: 0.8264 (tt0) cc_final: 0.7903 (tt0) REVERT: B 298 GLU cc_start: 0.7956 (tp30) cc_final: 0.7530 (tp30) REVERT: B 301 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8298 (ttpt) REVERT: B 308 GLN cc_start: 0.8613 (tp40) cc_final: 0.8317 (tp40) REVERT: C 1 MET cc_start: 0.8114 (tpt) cc_final: 0.7713 (tpt) REVERT: C 5 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8192 (mt) REVERT: C 6 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8141 (mtmm) REVERT: C 18 SER cc_start: 0.8429 (m) cc_final: 0.8016 (p) REVERT: C 32 SER cc_start: 0.8024 (m) cc_final: 0.7672 (p) REVERT: C 53 GLU cc_start: 0.7473 (pt0) cc_final: 0.7194 (pt0) REVERT: C 109 ASP cc_start: 0.8314 (t70) cc_final: 0.8048 (t0) REVERT: C 203 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8764 (mmmt) REVERT: C 241 ASP cc_start: 0.8501 (t0) cc_final: 0.8297 (t0) REVERT: C 246 GLU cc_start: 0.7969 (pt0) cc_final: 0.7583 (pt0) REVERT: C 249 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8641 (mtmm) REVERT: C 264 ASP cc_start: 0.8094 (t70) cc_final: 0.7550 (t0) REVERT: C 268 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8330 (mttm) REVERT: C 275 GLU cc_start: 0.7823 (tt0) cc_final: 0.7485 (tt0) REVERT: C 288 GLU cc_start: 0.8121 (tt0) cc_final: 0.7856 (tt0) REVERT: C 316 GLU cc_start: 0.8145 (tp30) cc_final: 0.7821 (tp30) REVERT: D 62 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8671 (p) REVERT: D 93 LYS cc_start: 0.8235 (tppt) cc_final: 0.7942 (tppt) REVERT: D 190 GLU cc_start: 0.8126 (mp0) cc_final: 0.7761 (mp0) REVERT: D 215 MET cc_start: 0.8333 (mtp) cc_final: 0.8033 (mtt) REVERT: D 243 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: D 253 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7116 (tm-30) REVERT: D 256 GLU cc_start: 0.8101 (tt0) cc_final: 0.7852 (tt0) REVERT: D 269 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7815 (mm-30) REVERT: E 3 ASP cc_start: 0.8210 (p0) cc_final: 0.7978 (p0) REVERT: E 46 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8071 (mtp85) REVERT: E 48 GLN cc_start: 0.7788 (tt0) cc_final: 0.7539 (mt0) REVERT: E 104 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7185 (p) REVERT: E 140 GLN cc_start: 0.8448 (mp10) cc_final: 0.8026 (mp10) REVERT: E 173 LEU cc_start: 0.8525 (mp) cc_final: 0.8208 (mp) REVERT: E 182 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7482 (tm-30) REVERT: E 183 SER cc_start: 0.8390 (t) cc_final: 0.8031 (m) REVERT: E 190 GLU cc_start: 0.7632 (mp0) cc_final: 0.7220 (mp0) REVERT: E 201 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7186 (mtp85) REVERT: E 205 TYR cc_start: 0.7983 (m-80) cc_final: 0.7285 (m-80) REVERT: E 249 LYS cc_start: 0.8154 (mmpt) cc_final: 0.7623 (mmpt) REVERT: E 253 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7170 (tm-30) REVERT: E 269 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7454 (mm-30) REVERT: E 287 GLN cc_start: 0.7470 (tp40) cc_final: 0.6950 (tp40) REVERT: E 288 GLU cc_start: 0.7596 (pt0) cc_final: 0.7167 (pt0) REVERT: E 290 ASN cc_start: 0.7648 (p0) cc_final: 0.7402 (p0) REVERT: E 291 ASP cc_start: 0.7278 (p0) cc_final: 0.6812 (p0) REVERT: F 1 MET cc_start: 0.8418 (tpp) cc_final: 0.8114 (tpp) REVERT: F 18 SER cc_start: 0.8643 (m) cc_final: 0.8021 (p) REVERT: F 54 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7629 (mtmm) REVERT: F 59 SER cc_start: 0.8868 (m) cc_final: 0.7969 (p) REVERT: F 82 ASN cc_start: 0.9038 (t0) cc_final: 0.8814 (t0) REVERT: F 97 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7234 (mt-10) REVERT: F 138 TYR cc_start: 0.8256 (t80) cc_final: 0.7972 (t80) REVERT: F 139 GLU cc_start: 0.7820 (mp0) cc_final: 0.7246 (mp0) REVERT: F 173 LEU cc_start: 0.8535 (tp) cc_final: 0.8297 (tt) REVERT: F 190 GLU cc_start: 0.7715 (mp0) cc_final: 0.7106 (mp0) REVERT: F 209 GLU cc_start: 0.8022 (tt0) cc_final: 0.7649 (tt0) REVERT: F 236 THR cc_start: 0.8876 (t) cc_final: 0.8510 (p) REVERT: F 249 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7996 (mtmt) REVERT: F 265 LEU cc_start: 0.8542 (mt) cc_final: 0.8338 (mp) REVERT: F 295 ASN cc_start: 0.8354 (t0) cc_final: 0.8094 (t0) REVERT: G 6 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8380 (ttpt) REVERT: G 8 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: G 48 GLN cc_start: 0.7421 (pt0) cc_final: 0.6785 (pt0) REVERT: G 54 LYS cc_start: 0.6694 (pttm) cc_final: 0.6228 (pttm) REVERT: G 72 GLU cc_start: 0.7655 (mp0) cc_final: 0.7152 (mp0) REVERT: G 162 MET cc_start: -0.1849 (tpp) cc_final: -0.2406 (tpp) REVERT: G 177 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7778 (p) REVERT: G 181 VAL cc_start: 0.8746 (t) cc_final: 0.8352 (p) REVERT: G 182 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7903 (mt-10) REVERT: G 183 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.8014 (p) REVERT: G 194 TYR cc_start: 0.8598 (t80) cc_final: 0.8212 (t80) REVERT: G 198 ASN cc_start: 0.8102 (m-40) cc_final: 0.7853 (t0) REVERT: G 216 LYS cc_start: 0.8238 (tppt) cc_final: 0.7852 (tppt) REVERT: G 267 ASN cc_start: 0.8356 (m-40) cc_final: 0.8116 (m-40) REVERT: G 268 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7566 (mtmt) REVERT: G 272 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7623 (mtm180) REVERT: G 275 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: G 288 GLU cc_start: 0.8214 (tp30) cc_final: 0.7714 (tp30) REVERT: G 295 ASN cc_start: 0.7484 (t0) cc_final: 0.7043 (t0) REVERT: H 13 ASP cc_start: 0.7678 (p0) cc_final: 0.7470 (p0) REVERT: H 24 ILE cc_start: 0.8910 (mt) cc_final: 0.8500 (tt) REVERT: H 39 TYR cc_start: 0.8866 (m-80) cc_final: 0.8470 (m-80) REVERT: H 68 ARG cc_start: 0.8719 (mtp180) cc_final: 0.8511 (mtp180) REVERT: H 180 TYR cc_start: 0.8809 (p90) cc_final: 0.8387 (p90) REVERT: H 209 SER cc_start: 0.8554 (p) cc_final: 0.8323 (m) REVERT: I 33 GLU cc_start: 0.7899 (pp20) cc_final: 0.7454 (pp20) REVERT: I 84 ASN cc_start: 0.7995 (m-40) cc_final: 0.7505 (m110) REVERT: I 158 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6939 (ttp80) REVERT: I 220 ASP cc_start: 0.7858 (m-30) cc_final: 0.7191 (m-30) REVERT: I 235 ASN cc_start: 0.8544 (t0) cc_final: 0.8320 (t0) REVERT: I 241 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7519 (mmmt) REVERT: I 271 ASP cc_start: 0.8171 (m-30) cc_final: 0.7909 (t0) REVERT: I 284 TYR cc_start: 0.7732 (m-80) cc_final: 0.6924 (m-80) REVERT: I 491 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: I 496 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7702 (ttm170) REVERT: I 512 GLN cc_start: 0.7999 (tp40) cc_final: 0.7618 (tm-30) REVERT: I 574 SER cc_start: 0.8633 (t) cc_final: 0.8093 (p) REVERT: I 600 TYR cc_start: 0.8667 (m-80) cc_final: 0.8463 (m-80) REVERT: I 605 TYR cc_start: 0.7829 (m-80) cc_final: 0.7525 (m-80) REVERT: I 620 TYR cc_start: 0.8159 (m-80) cc_final: 0.7317 (m-80) REVERT: I 639 MET cc_start: 0.7675 (mmp) cc_final: 0.7436 (mmp) REVERT: I 668 ASP cc_start: 0.7114 (p0) cc_final: 0.6838 (p0) REVERT: I 696 LEU cc_start: 0.8623 (mt) cc_final: 0.8379 (mm) REVERT: I 712 MET cc_start: 0.8658 (mtm) cc_final: 0.8326 (mtt) REVERT: I 746 VAL cc_start: 0.8697 (p) cc_final: 0.8449 (p) REVERT: I 750 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8650 (m) REVERT: I 754 ASN cc_start: 0.8655 (m-40) cc_final: 0.8325 (m-40) REVERT: I 772 LYS cc_start: 0.7584 (mptp) cc_final: 0.7254 (mptp) REVERT: I 776 GLN cc_start: 0.8100 (mp10) cc_final: 0.7690 (mp10) REVERT: I 783 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7676 (tm-30) REVERT: I 802 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8296 (ttp80) REVERT: I 827 ASN cc_start: 0.8062 (t0) cc_final: 0.7803 (t0) REVERT: I 830 MET cc_start: 0.8081 (mtm) cc_final: 0.7764 (mtm) REVERT: I 833 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8430 (ttmm) REVERT: I 851 GLU cc_start: 0.8136 (tp30) cc_final: 0.7904 (tp30) REVERT: I 870 GLU cc_start: 0.7891 (tp30) cc_final: 0.7326 (tp30) REVERT: I 881 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7720 (pp20) REVERT: I 901 VAL cc_start: 0.8801 (t) cc_final: 0.8564 (p) REVERT: I 902 TYR cc_start: 0.8705 (p90) cc_final: 0.8490 (p90) REVERT: I 909 ASP cc_start: 0.7628 (p0) cc_final: 0.7418 (p0) REVERT: I 916 THR cc_start: 0.8258 (p) cc_final: 0.8055 (m) REVERT: I 920 GLN cc_start: 0.8432 (mt0) cc_final: 0.8085 (mt0) REVERT: I 923 GLU cc_start: 0.7925 (pp20) cc_final: 0.7652 (pp20) REVERT: I 942 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8900 (mmmt) REVERT: J 5 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.4286 (pt) REVERT: J 63 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8368 (tp) REVERT: J 64 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8114 (tm-30) REVERT: J 67 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (mt) REVERT: J 88 ARG cc_start: 0.7976 (mtt180) cc_final: 0.7538 (mtt180) REVERT: J 89 GLN cc_start: 0.8266 (mm110) cc_final: 0.8012 (mm110) REVERT: J 90 LEU cc_start: 0.8407 (tt) cc_final: 0.8162 (tt) REVERT: J 91 GLN cc_start: 0.8535 (mt0) cc_final: 0.8228 (mt0) REVERT: J 92 GLU cc_start: 0.8176 (tp30) cc_final: 0.7689 (tp30) REVERT: J 93 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8482 (tt) REVERT: J 94 GLU cc_start: 0.8203 (pt0) cc_final: 0.7797 (pt0) REVERT: J 120 GLN cc_start: 0.8378 (tp40) cc_final: 0.8017 (tt0) REVERT: J 140 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7235 (tm-30) REVERT: J 143 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7371 (tp40) REVERT: K 13 GLU cc_start: 0.7125 (tt0) cc_final: 0.6869 (tt0) REVERT: K 22 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6076 (pp20) REVERT: K 41 GLU cc_start: 0.7198 (tp30) cc_final: 0.6595 (tp30) REVERT: K 52 GLU cc_start: 0.7885 (pp20) cc_final: 0.7272 (pp20) REVERT: K 71 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6529 (pm20) REVERT: K 94 GLU cc_start: 0.7745 (tp30) cc_final: 0.7117 (tp30) REVERT: K 131 GLU cc_start: 0.7565 (tp30) cc_final: 0.7106 (tp30) outliers start: 132 outliers final: 85 residues processed: 1028 average time/residue: 0.2090 time to fit residues: 327.6302 Evaluate side-chains 1078 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 972 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 821 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 940 MET Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 136 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 289 optimal weight: 0.0970 chunk 326 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 68 GLN D 295 ASN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113702 restraints weight = 44049.032| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.94 r_work: 0.3318 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29660 Z= 0.188 Angle : 0.656 9.723 40467 Z= 0.339 Chirality : 0.045 0.353 4565 Planarity : 0.004 0.047 4974 Dihedral : 15.285 179.583 4938 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.38 % Allowed : 21.27 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.16 (0.14), residues: 3399 helix: 1.20 (0.14), residues: 1475 sheet: -0.22 (0.23), residues: 409 loop : -0.86 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 272 TYR 0.023 0.002 TYR I 844 PHE 0.032 0.002 PHE E 151 TRP 0.034 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00414 (29660) covalent geometry : angle 0.65636 (40467) hydrogen bonds : bond 0.03667 ( 1334) hydrogen bonds : angle 4.49072 ( 3811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 973 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8622 (mt0) REVERT: A 32 SER cc_start: 0.8183 (t) cc_final: 0.7819 (p) REVERT: A 57 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7925 (mm-40) REVERT: A 78 GLU cc_start: 0.8213 (tt0) cc_final: 0.7992 (tt0) REVERT: A 142 HIS cc_start: 0.8760 (p-80) cc_final: 0.8004 (p-80) REVERT: A 155 THR cc_start: 0.8169 (m) cc_final: 0.7891 (t) REVERT: A 180 THR cc_start: 0.8313 (p) cc_final: 0.8062 (t) REVERT: A 253 GLU cc_start: 0.8063 (tp30) cc_final: 0.7511 (tp30) REVERT: A 272 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7919 (ttt180) REVERT: A 298 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: A 308 GLN cc_start: 0.8269 (tp40) cc_final: 0.7872 (tp-100) REVERT: B 109 ASP cc_start: 0.8039 (t0) cc_final: 0.7713 (t0) REVERT: B 123 GLU cc_start: 0.7818 (tp30) cc_final: 0.7606 (tp30) REVERT: B 162 MET cc_start: 0.8537 (mmt) cc_final: 0.8193 (mmm) REVERT: B 190 GLU cc_start: 0.8043 (mp0) cc_final: 0.7753 (mp0) REVERT: B 248 ASN cc_start: 0.8261 (m110) cc_final: 0.8003 (p0) REVERT: B 253 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 256 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 268 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8543 (mtmm) REVERT: B 287 GLN cc_start: 0.8386 (tp40) cc_final: 0.8139 (tp40) REVERT: B 288 GLU cc_start: 0.8266 (tt0) cc_final: 0.7934 (tt0) REVERT: B 298 GLU cc_start: 0.8001 (tp30) cc_final: 0.7729 (tp30) REVERT: B 308 GLN cc_start: 0.8611 (tp40) cc_final: 0.8320 (tp40) REVERT: C 1 MET cc_start: 0.8139 (tpt) cc_final: 0.7775 (tpt) REVERT: C 5 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8207 (mt) REVERT: C 6 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8133 (mtmm) REVERT: C 18 SER cc_start: 0.8392 (m) cc_final: 0.8030 (p) REVERT: C 32 SER cc_start: 0.8182 (m) cc_final: 0.7861 (p) REVERT: C 53 GLU cc_start: 0.7504 (pt0) cc_final: 0.6849 (pt0) REVERT: C 54 LYS cc_start: 0.8345 (mptt) cc_final: 0.7877 (mptt) REVERT: C 109 ASP cc_start: 0.8307 (t70) cc_final: 0.8032 (t0) REVERT: C 203 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8749 (mmmt) REVERT: C 241 ASP cc_start: 0.8537 (t0) cc_final: 0.8308 (t0) REVERT: C 246 GLU cc_start: 0.7852 (pt0) cc_final: 0.7519 (pt0) REVERT: C 264 ASP cc_start: 0.8093 (t70) cc_final: 0.7557 (t0) REVERT: C 268 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8345 (mttm) REVERT: C 275 GLU cc_start: 0.7849 (tt0) cc_final: 0.7495 (tt0) REVERT: C 288 GLU cc_start: 0.8129 (tt0) cc_final: 0.7847 (tt0) REVERT: C 316 GLU cc_start: 0.8148 (tp30) cc_final: 0.7837 (tp30) REVERT: D 62 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8683 (p) REVERT: D 68 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: D 72 GLU cc_start: 0.7773 (mp0) cc_final: 0.7362 (mp0) REVERT: D 93 LYS cc_start: 0.8223 (tppt) cc_final: 0.7937 (tppt) REVERT: D 130 ASP cc_start: 0.7712 (t0) cc_final: 0.7193 (t0) REVERT: D 190 GLU cc_start: 0.8138 (mp0) cc_final: 0.7734 (mp0) REVERT: D 215 MET cc_start: 0.8320 (mtp) cc_final: 0.8031 (mtt) REVERT: D 243 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: D 253 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7123 (tm-30) REVERT: D 256 GLU cc_start: 0.8090 (tt0) cc_final: 0.7837 (tt0) REVERT: D 269 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 3 ASP cc_start: 0.8198 (p0) cc_final: 0.7979 (p0) REVERT: E 46 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8079 (mtp85) REVERT: E 48 GLN cc_start: 0.7800 (tt0) cc_final: 0.7552 (mt0) REVERT: E 90 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (tppt) REVERT: E 104 CYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7187 (p) REVERT: E 140 GLN cc_start: 0.8448 (mp10) cc_final: 0.8017 (mp10) REVERT: E 173 LEU cc_start: 0.8532 (mp) cc_final: 0.8210 (mp) REVERT: E 182 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: E 183 SER cc_start: 0.8417 (t) cc_final: 0.8039 (m) REVERT: E 190 GLU cc_start: 0.7616 (mp0) cc_final: 0.7203 (mp0) REVERT: E 201 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7311 (mtp85) REVERT: E 205 TYR cc_start: 0.7997 (m-80) cc_final: 0.7323 (m-80) REVERT: E 249 LYS cc_start: 0.8187 (mmpt) cc_final: 0.7664 (mmpt) REVERT: E 253 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7174 (tm-30) REVERT: E 269 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7446 (mm-30) REVERT: E 287 GLN cc_start: 0.7513 (tp40) cc_final: 0.6910 (tp40) REVERT: E 288 GLU cc_start: 0.7636 (pt0) cc_final: 0.7170 (pt0) REVERT: E 290 ASN cc_start: 0.7595 (p0) cc_final: 0.7366 (p0) REVERT: E 291 ASP cc_start: 0.7300 (p0) cc_final: 0.6841 (p0) REVERT: F 1 MET cc_start: 0.8436 (tpp) cc_final: 0.8077 (tpp) REVERT: F 6 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7665 (mtpp) REVERT: F 18 SER cc_start: 0.8572 (m) cc_final: 0.7982 (p) REVERT: F 54 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7611 (mtmm) REVERT: F 59 SER cc_start: 0.8873 (m) cc_final: 0.7976 (p) REVERT: F 66 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8024 (mpt180) REVERT: F 97 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7266 (mt-10) REVERT: F 138 TYR cc_start: 0.8229 (t80) cc_final: 0.7882 (t80) REVERT: F 139 GLU cc_start: 0.7883 (mp0) cc_final: 0.7300 (mp0) REVERT: F 173 LEU cc_start: 0.8517 (tp) cc_final: 0.8295 (tt) REVERT: F 186 ASP cc_start: 0.7416 (p0) cc_final: 0.7176 (p0) REVERT: F 190 GLU cc_start: 0.7692 (mp0) cc_final: 0.7238 (mp0) REVERT: F 209 GLU cc_start: 0.8035 (tt0) cc_final: 0.7622 (tt0) REVERT: F 236 THR cc_start: 0.8874 (t) cc_final: 0.8507 (p) REVERT: F 249 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8005 (mtmt) REVERT: F 265 LEU cc_start: 0.8591 (mt) cc_final: 0.8379 (mp) REVERT: F 295 ASN cc_start: 0.8351 (t0) cc_final: 0.8100 (t0) REVERT: F 298 GLU cc_start: 0.8239 (mp0) cc_final: 0.7983 (mt-10) REVERT: G 6 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8363 (ttpt) REVERT: G 8 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: G 48 GLN cc_start: 0.7412 (pt0) cc_final: 0.6722 (pt0) REVERT: G 54 LYS cc_start: 0.6746 (pttm) cc_final: 0.6143 (pttm) REVERT: G 72 GLU cc_start: 0.7719 (mp0) cc_final: 0.7191 (mp0) REVERT: G 128 TYR cc_start: 0.8316 (m-80) cc_final: 0.7978 (m-80) REVERT: G 162 MET cc_start: -0.1845 (tpp) cc_final: -0.2406 (tpp) REVERT: G 177 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7741 (p) REVERT: G 181 VAL cc_start: 0.8747 (t) cc_final: 0.8372 (p) REVERT: G 182 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7898 (mt-10) REVERT: G 183 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8036 (p) REVERT: G 185 ARG cc_start: 0.8049 (ptp-170) cc_final: 0.7763 (mtp85) REVERT: G 194 TYR cc_start: 0.8567 (t80) cc_final: 0.8166 (t80) REVERT: G 198 ASN cc_start: 0.8194 (m-40) cc_final: 0.7860 (t0) REVERT: G 216 LYS cc_start: 0.8235 (tppt) cc_final: 0.7799 (tppt) REVERT: G 240 TYR cc_start: 0.8555 (t80) cc_final: 0.8183 (t80) REVERT: G 256 GLU cc_start: 0.7455 (pp20) cc_final: 0.7232 (pp20) REVERT: G 268 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7614 (mtmt) REVERT: G 275 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7064 (mt-10) REVERT: G 288 GLU cc_start: 0.8233 (tp30) cc_final: 0.7800 (tp30) REVERT: G 295 ASN cc_start: 0.7517 (t0) cc_final: 0.7061 (t0) REVERT: H 13 ASP cc_start: 0.7694 (p0) cc_final: 0.7491 (p0) REVERT: H 24 ILE cc_start: 0.8915 (mt) cc_final: 0.8505 (tt) REVERT: H 29 GLU cc_start: 0.8293 (tp30) cc_final: 0.8061 (tp30) REVERT: H 39 TYR cc_start: 0.8896 (m-80) cc_final: 0.8540 (m-80) REVERT: H 180 TYR cc_start: 0.8770 (p90) cc_final: 0.8372 (p90) REVERT: H 209 SER cc_start: 0.8563 (p) cc_final: 0.8336 (m) REVERT: I 26 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7543 (mt0) REVERT: I 33 GLU cc_start: 0.7889 (pp20) cc_final: 0.7374 (pp20) REVERT: I 84 ASN cc_start: 0.7982 (m-40) cc_final: 0.7504 (m-40) REVERT: I 158 ARG cc_start: 0.7266 (ttp80) cc_final: 0.6909 (ttp80) REVERT: I 220 ASP cc_start: 0.7859 (m-30) cc_final: 0.7196 (m-30) REVERT: I 235 ASN cc_start: 0.8534 (t0) cc_final: 0.8327 (t0) REVERT: I 241 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7543 (mmmt) REVERT: I 271 ASP cc_start: 0.8220 (m-30) cc_final: 0.7950 (t0) REVERT: I 284 TYR cc_start: 0.7726 (m-80) cc_final: 0.6936 (m-80) REVERT: I 491 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: I 495 ASP cc_start: 0.8119 (p0) cc_final: 0.7783 (p0) REVERT: I 496 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7758 (ttm170) REVERT: I 512 GLN cc_start: 0.8095 (tp40) cc_final: 0.7711 (tm-30) REVERT: I 574 SER cc_start: 0.8588 (t) cc_final: 0.8057 (p) REVERT: I 576 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7543 (tm-30) REVERT: I 600 TYR cc_start: 0.8731 (m-80) cc_final: 0.8476 (m-80) REVERT: I 605 TYR cc_start: 0.7824 (m-80) cc_final: 0.7551 (m-80) REVERT: I 620 TYR cc_start: 0.8170 (m-80) cc_final: 0.7345 (m-80) REVERT: I 639 MET cc_start: 0.7626 (mmp) cc_final: 0.7372 (mmp) REVERT: I 668 ASP cc_start: 0.7125 (p0) cc_final: 0.6829 (p0) REVERT: I 696 LEU cc_start: 0.8602 (mt) cc_final: 0.8376 (mm) REVERT: I 711 SER cc_start: 0.8596 (t) cc_final: 0.8270 (t) REVERT: I 746 VAL cc_start: 0.8704 (p) cc_final: 0.8450 (p) REVERT: I 750 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8638 (m) REVERT: I 754 ASN cc_start: 0.8667 (m-40) cc_final: 0.8326 (m-40) REVERT: I 772 LYS cc_start: 0.7627 (mptp) cc_final: 0.7270 (mptp) REVERT: I 776 GLN cc_start: 0.8134 (mp10) cc_final: 0.7702 (mp10) REVERT: I 783 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7639 (tm-30) REVERT: I 802 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8283 (ttp80) REVERT: I 827 ASN cc_start: 0.8055 (t0) cc_final: 0.7727 (t0) REVERT: I 830 MET cc_start: 0.8091 (mtm) cc_final: 0.7747 (mtm) REVERT: I 833 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8369 (ttmm) REVERT: I 851 GLU cc_start: 0.8148 (tp30) cc_final: 0.7925 (tp30) REVERT: I 870 GLU cc_start: 0.7910 (tp30) cc_final: 0.7348 (tp30) REVERT: I 881 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7736 (pp20) REVERT: I 901 VAL cc_start: 0.8812 (t) cc_final: 0.8577 (p) REVERT: I 902 TYR cc_start: 0.8719 (p90) cc_final: 0.8509 (p90) REVERT: I 909 ASP cc_start: 0.7605 (p0) cc_final: 0.7404 (p0) REVERT: I 920 GLN cc_start: 0.8443 (mt0) cc_final: 0.8092 (mt0) REVERT: I 923 GLU cc_start: 0.7929 (pp20) cc_final: 0.7653 (pp20) REVERT: I 942 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8894 (mmmt) REVERT: J 5 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.4325 (pt) REVERT: J 22 GLU cc_start: 0.7627 (pt0) cc_final: 0.7071 (pm20) REVERT: J 53 GLU cc_start: 0.7736 (mp0) cc_final: 0.7403 (mp0) REVERT: J 67 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7733 (mt) REVERT: J 88 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7599 (mtt180) REVERT: J 89 GLN cc_start: 0.8288 (mm110) cc_final: 0.8033 (mm110) REVERT: J 92 GLU cc_start: 0.8109 (tp30) cc_final: 0.7579 (tp30) REVERT: J 93 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8476 (tt) REVERT: J 120 GLN cc_start: 0.8384 (tp40) cc_final: 0.8035 (tt0) REVERT: J 140 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7304 (tm-30) REVERT: J 143 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: K 13 GLU cc_start: 0.7140 (tt0) cc_final: 0.6888 (tt0) REVERT: K 22 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6148 (pp20) REVERT: K 41 GLU cc_start: 0.7195 (tp30) cc_final: 0.6585 (tp30) REVERT: K 52 GLU cc_start: 0.7840 (pp20) cc_final: 0.7255 (pp20) REVERT: K 71 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: K 94 GLU cc_start: 0.7736 (tp30) cc_final: 0.7160 (tp30) REVERT: K 131 GLU cc_start: 0.7581 (tp30) cc_final: 0.7097 (tp30) outliers start: 130 outliers final: 91 residues processed: 1025 average time/residue: 0.2102 time to fit residues: 327.9172 Evaluate side-chains 1082 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 969 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 821 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 940 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 14 optimal weight: 0.6980 chunk 283 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 266 optimal weight: 0.1980 chunk 309 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 250 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 292 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN E 295 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS J 64 GLN J 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114812 restraints weight = 43931.517| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.89 r_work: 0.3336 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29660 Z= 0.149 Angle : 0.647 10.153 40467 Z= 0.331 Chirality : 0.044 0.345 4565 Planarity : 0.004 0.046 4974 Dihedral : 15.241 179.283 4933 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.80 % Allowed : 22.38 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.32 (0.15), residues: 3399 helix: 1.35 (0.14), residues: 1448 sheet: -0.21 (0.23), residues: 409 loop : -0.73 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 28 TYR 0.023 0.001 TYR I 844 PHE 0.034 0.001 PHE E 151 TRP 0.034 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00328 (29660) covalent geometry : angle 0.64703 (40467) hydrogen bonds : bond 0.03510 ( 1334) hydrogen bonds : angle 4.42941 ( 3811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 985 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8591 (mt0) REVERT: A 32 SER cc_start: 0.8186 (t) cc_final: 0.7828 (p) REVERT: A 36 PHE cc_start: 0.8962 (m-80) cc_final: 0.8652 (m-80) REVERT: A 57 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7909 (mm-40) REVERT: A 78 GLU cc_start: 0.8200 (tt0) cc_final: 0.7975 (tt0) REVERT: A 139 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 142 HIS cc_start: 0.8753 (p-80) cc_final: 0.7961 (p-80) REVERT: A 155 THR cc_start: 0.8120 (m) cc_final: 0.7879 (t) REVERT: A 180 THR cc_start: 0.8307 (p) cc_final: 0.8052 (t) REVERT: A 253 GLU cc_start: 0.8031 (tp30) cc_final: 0.7487 (tp30) REVERT: A 272 ARG cc_start: 0.8148 (tpt170) cc_final: 0.7907 (ttt180) REVERT: A 290 ASN cc_start: 0.8629 (m-40) cc_final: 0.8194 (m-40) REVERT: A 298 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: A 308 GLN cc_start: 0.8225 (tp40) cc_final: 0.7968 (tp-100) REVERT: B 109 ASP cc_start: 0.8012 (t0) cc_final: 0.7684 (t0) REVERT: B 126 LYS cc_start: 0.8749 (mttp) cc_final: 0.8455 (mmtm) REVERT: B 162 MET cc_start: 0.8513 (mmt) cc_final: 0.8172 (mmm) REVERT: B 190 GLU cc_start: 0.8005 (mp0) cc_final: 0.7730 (mp0) REVERT: B 253 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 256 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 268 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8559 (mtmm) REVERT: B 287 GLN cc_start: 0.8363 (tp40) cc_final: 0.8048 (tp40) REVERT: B 288 GLU cc_start: 0.8237 (tt0) cc_final: 0.7900 (tt0) REVERT: B 298 GLU cc_start: 0.7985 (tp30) cc_final: 0.7555 (tp30) REVERT: B 301 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8289 (ttpt) REVERT: B 308 GLN cc_start: 0.8593 (tp40) cc_final: 0.8294 (tp40) REVERT: C 1 MET cc_start: 0.8141 (tpt) cc_final: 0.7715 (tpt) REVERT: C 5 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 6 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8099 (mtmm) REVERT: C 18 SER cc_start: 0.8373 (m) cc_final: 0.8009 (p) REVERT: C 53 GLU cc_start: 0.7482 (pt0) cc_final: 0.7219 (pt0) REVERT: C 109 ASP cc_start: 0.8262 (t70) cc_final: 0.7997 (t0) REVERT: C 241 ASP cc_start: 0.8503 (t0) cc_final: 0.8294 (t0) REVERT: C 246 GLU cc_start: 0.7835 (pt0) cc_final: 0.7532 (pt0) REVERT: C 264 ASP cc_start: 0.8102 (t70) cc_final: 0.7550 (t0) REVERT: C 268 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8325 (mttm) REVERT: C 275 GLU cc_start: 0.7814 (tt0) cc_final: 0.7485 (tt0) REVERT: C 288 GLU cc_start: 0.8091 (tt0) cc_final: 0.7817 (tt0) REVERT: C 316 GLU cc_start: 0.8145 (tp30) cc_final: 0.7842 (tp30) REVERT: D 62 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8670 (p) REVERT: D 72 GLU cc_start: 0.7728 (mp0) cc_final: 0.7371 (mp0) REVERT: D 93 LYS cc_start: 0.8194 (tppt) cc_final: 0.7914 (tppt) REVERT: D 190 GLU cc_start: 0.8130 (mp0) cc_final: 0.7719 (mp0) REVERT: D 215 MET cc_start: 0.8300 (mtp) cc_final: 0.8005 (mtt) REVERT: D 243 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: D 256 GLU cc_start: 0.8086 (tt0) cc_final: 0.7840 (tt0) REVERT: E 3 ASP cc_start: 0.8140 (p0) cc_final: 0.7925 (p0) REVERT: E 46 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.8018 (mtp85) REVERT: E 48 GLN cc_start: 0.7778 (tt0) cc_final: 0.7535 (mt0) REVERT: E 140 GLN cc_start: 0.8425 (mp10) cc_final: 0.7991 (mp10) REVERT: E 173 LEU cc_start: 0.8523 (mp) cc_final: 0.8206 (mp) REVERT: E 182 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7494 (tm-30) REVERT: E 183 SER cc_start: 0.8415 (t) cc_final: 0.8101 (m) REVERT: E 190 GLU cc_start: 0.7602 (mp0) cc_final: 0.7202 (mp0) REVERT: E 205 TYR cc_start: 0.7986 (m-80) cc_final: 0.7329 (m-80) REVERT: E 249 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7948 (mmpt) REVERT: E 269 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7442 (mm-30) REVERT: E 287 GLN cc_start: 0.7499 (tp40) cc_final: 0.6884 (tp40) REVERT: E 288 GLU cc_start: 0.7606 (pt0) cc_final: 0.7148 (pt0) REVERT: E 290 ASN cc_start: 0.7566 (p0) cc_final: 0.7344 (p0) REVERT: E 291 ASP cc_start: 0.7268 (p0) cc_final: 0.6811 (p0) REVERT: F 1 MET cc_start: 0.8384 (tpp) cc_final: 0.8071 (tpp) REVERT: F 6 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7663 (mtpp) REVERT: F 18 SER cc_start: 0.8533 (m) cc_final: 0.7906 (p) REVERT: F 54 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7624 (mtmm) REVERT: F 59 SER cc_start: 0.8878 (m) cc_final: 0.7962 (p) REVERT: F 66 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7980 (mpt180) REVERT: F 97 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7181 (mt-10) REVERT: F 138 TYR cc_start: 0.8203 (t80) cc_final: 0.7910 (t80) REVERT: F 139 GLU cc_start: 0.7850 (mp0) cc_final: 0.7270 (mp0) REVERT: F 173 LEU cc_start: 0.8477 (tp) cc_final: 0.8264 (tt) REVERT: F 190 GLU cc_start: 0.7651 (mp0) cc_final: 0.7169 (mp0) REVERT: F 209 GLU cc_start: 0.7966 (tt0) cc_final: 0.7567 (tt0) REVERT: F 236 THR cc_start: 0.8871 (t) cc_final: 0.8500 (p) REVERT: F 249 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7958 (mtmt) REVERT: F 265 LEU cc_start: 0.8568 (mt) cc_final: 0.8339 (mp) REVERT: F 295 ASN cc_start: 0.8338 (t0) cc_final: 0.8082 (t0) REVERT: G 8 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: G 22 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8220 (t) REVERT: G 48 GLN cc_start: 0.7262 (pt0) cc_final: 0.6718 (pt0) REVERT: G 54 LYS cc_start: 0.6690 (pttm) cc_final: 0.6102 (pttm) REVERT: G 72 GLU cc_start: 0.7699 (mp0) cc_final: 0.7152 (mp0) REVERT: G 162 MET cc_start: -0.1888 (tpp) cc_final: -0.2480 (tpp) REVERT: G 177 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7701 (p) REVERT: G 181 VAL cc_start: 0.8733 (t) cc_final: 0.8371 (p) REVERT: G 182 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7837 (mt-10) REVERT: G 194 TYR cc_start: 0.8549 (t80) cc_final: 0.8202 (t80) REVERT: G 198 ASN cc_start: 0.8154 (m-40) cc_final: 0.7798 (t0) REVERT: G 216 LYS cc_start: 0.8216 (tppt) cc_final: 0.7846 (tppt) REVERT: G 243 MET cc_start: 0.7318 (mtm) cc_final: 0.7108 (mtm) REVERT: G 256 GLU cc_start: 0.7420 (pp20) cc_final: 0.7115 (pp20) REVERT: G 268 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7630 (mtmt) REVERT: G 275 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7038 (mt-10) REVERT: G 288 GLU cc_start: 0.8202 (tp30) cc_final: 0.7820 (tp30) REVERT: G 295 ASN cc_start: 0.7400 (t0) cc_final: 0.6946 (t0) REVERT: H 13 ASP cc_start: 0.7693 (p0) cc_final: 0.7482 (p0) REVERT: H 24 ILE cc_start: 0.8917 (mt) cc_final: 0.8505 (tt) REVERT: H 29 GLU cc_start: 0.8277 (tp30) cc_final: 0.8033 (tp30) REVERT: H 39 TYR cc_start: 0.8867 (m-80) cc_final: 0.8518 (m-80) REVERT: H 180 TYR cc_start: 0.8750 (p90) cc_final: 0.8297 (p90) REVERT: H 209 SER cc_start: 0.8534 (p) cc_final: 0.8308 (m) REVERT: I 26 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7548 (mm-40) REVERT: I 33 GLU cc_start: 0.7830 (pp20) cc_final: 0.7312 (pp20) REVERT: I 84 ASN cc_start: 0.7996 (m-40) cc_final: 0.7510 (m110) REVERT: I 158 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6901 (ttp80) REVERT: I 241 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7541 (mmmt) REVERT: I 284 TYR cc_start: 0.7721 (m-80) cc_final: 0.6976 (m-80) REVERT: I 487 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7802 (tmm160) REVERT: I 491 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: I 496 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7727 (ttm170) REVERT: I 512 GLN cc_start: 0.8050 (tp40) cc_final: 0.7664 (tm-30) REVERT: I 574 SER cc_start: 0.8540 (t) cc_final: 0.8022 (p) REVERT: I 600 TYR cc_start: 0.8719 (m-80) cc_final: 0.8501 (m-80) REVERT: I 605 TYR cc_start: 0.7797 (m-80) cc_final: 0.7578 (m-80) REVERT: I 620 TYR cc_start: 0.8156 (m-80) cc_final: 0.7308 (m-80) REVERT: I 639 MET cc_start: 0.7541 (mmp) cc_final: 0.7312 (mmp) REVERT: I 668 ASP cc_start: 0.7084 (p0) cc_final: 0.6802 (p0) REVERT: I 696 LEU cc_start: 0.8569 (mt) cc_final: 0.8360 (mm) REVERT: I 707 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8541 (mt) REVERT: I 746 VAL cc_start: 0.8679 (p) cc_final: 0.8426 (p) REVERT: I 750 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8633 (m) REVERT: I 754 ASN cc_start: 0.8648 (m-40) cc_final: 0.8272 (m110) REVERT: I 772 LYS cc_start: 0.7514 (mptp) cc_final: 0.7169 (mptp) REVERT: I 776 GLN cc_start: 0.8074 (mp10) cc_final: 0.7696 (mp10) REVERT: I 783 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7610 (tm-30) REVERT: I 802 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8253 (ttp80) REVERT: I 827 ASN cc_start: 0.8032 (t0) cc_final: 0.7580 (t0) REVERT: I 830 MET cc_start: 0.8064 (mtm) cc_final: 0.7712 (mtm) REVERT: I 833 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8349 (ttmm) REVERT: I 851 GLU cc_start: 0.8097 (tp30) cc_final: 0.7852 (tp30) REVERT: I 870 GLU cc_start: 0.7831 (tp30) cc_final: 0.7265 (tp30) REVERT: I 881 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7727 (pp20) REVERT: I 901 VAL cc_start: 0.8806 (t) cc_final: 0.8568 (p) REVERT: I 902 TYR cc_start: 0.8712 (p90) cc_final: 0.8500 (p90) REVERT: I 920 GLN cc_start: 0.8454 (mt0) cc_final: 0.8099 (mt0) REVERT: I 923 GLU cc_start: 0.7918 (pp20) cc_final: 0.7635 (pp20) REVERT: I 942 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8877 (mmmt) REVERT: J 5 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.4371 (pt) REVERT: J 22 GLU cc_start: 0.7638 (pt0) cc_final: 0.7123 (pm20) REVERT: J 53 GLU cc_start: 0.7721 (mp0) cc_final: 0.7397 (mp0) REVERT: J 88 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7125 (mtt180) REVERT: J 89 GLN cc_start: 0.8317 (mm110) cc_final: 0.8101 (mm110) REVERT: J 91 GLN cc_start: 0.8453 (mt0) cc_final: 0.8131 (mt0) REVERT: J 92 GLU cc_start: 0.8117 (tp30) cc_final: 0.7583 (tp30) REVERT: J 93 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8494 (tt) REVERT: J 120 GLN cc_start: 0.8360 (tp40) cc_final: 0.8019 (tt0) REVERT: J 140 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7343 (tm-30) REVERT: J 143 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7375 (tp40) REVERT: K 13 GLU cc_start: 0.7057 (tt0) cc_final: 0.6818 (tt0) REVERT: K 22 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: K 41 GLU cc_start: 0.7181 (tp30) cc_final: 0.6571 (tp30) REVERT: K 52 GLU cc_start: 0.7810 (pp20) cc_final: 0.7232 (pp20) REVERT: K 71 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: K 94 GLU cc_start: 0.7732 (tp30) cc_final: 0.7173 (tp30) REVERT: K 131 GLU cc_start: 0.7471 (tp30) cc_final: 0.7008 (tp30) outliers start: 113 outliers final: 84 residues processed: 1027 average time/residue: 0.2076 time to fit residues: 326.2186 Evaluate side-chains 1084 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 982 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 501 GLN Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 821 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 940 MET Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 136 optimal weight: 0.7980 chunk 323 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 339 optimal weight: 4.9990 chunk 308 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 245 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 248 ASN D 68 GLN D 171 HIS E 10 GLN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 651 ASN J 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113894 restraints weight = 43813.474| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.88 r_work: 0.3333 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29660 Z= 0.198 Angle : 0.676 16.808 40467 Z= 0.345 Chirality : 0.045 0.347 4565 Planarity : 0.004 0.056 4974 Dihedral : 15.197 179.955 4931 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.77 % Allowed : 23.12 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.16 (0.14), residues: 3399 helix: 1.23 (0.14), residues: 1470 sheet: -0.15 (0.23), residues: 436 loop : -0.92 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 68 TYR 0.022 0.002 TYR I 844 PHE 0.034 0.002 PHE E 151 TRP 0.031 0.002 TRP I 154 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00436 (29660) covalent geometry : angle 0.67572 (40467) hydrogen bonds : bond 0.03651 ( 1334) hydrogen bonds : angle 4.47990 ( 3811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 978 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8554 (mt0) REVERT: A 32 SER cc_start: 0.8200 (t) cc_final: 0.7839 (p) REVERT: A 57 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7889 (mm-40) REVERT: A 78 GLU cc_start: 0.8181 (tt0) cc_final: 0.7962 (tt0) REVERT: A 139 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 142 HIS cc_start: 0.8766 (p-80) cc_final: 0.8041 (p-80) REVERT: A 155 THR cc_start: 0.8177 (m) cc_final: 0.7900 (t) REVERT: A 180 THR cc_start: 0.8307 (p) cc_final: 0.8071 (t) REVERT: A 253 GLU cc_start: 0.8021 (tp30) cc_final: 0.7476 (tp30) REVERT: A 272 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7894 (ttt180) REVERT: A 290 ASN cc_start: 0.8634 (m-40) cc_final: 0.8203 (m-40) REVERT: A 298 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: A 308 GLN cc_start: 0.8233 (tp40) cc_final: 0.7984 (tp-100) REVERT: B 109 ASP cc_start: 0.8016 (t0) cc_final: 0.7674 (t0) REVERT: B 123 GLU cc_start: 0.7742 (tp30) cc_final: 0.7407 (tp30) REVERT: B 162 MET cc_start: 0.8568 (mmt) cc_final: 0.8223 (mmm) REVERT: B 253 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 256 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 268 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8608 (mtmm) REVERT: B 287 GLN cc_start: 0.8361 (tp40) cc_final: 0.8042 (tp40) REVERT: B 288 GLU cc_start: 0.8220 (tt0) cc_final: 0.7887 (tt0) REVERT: B 298 GLU cc_start: 0.7979 (tp30) cc_final: 0.7582 (tp30) REVERT: B 301 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8311 (ttpt) REVERT: B 308 GLN cc_start: 0.8576 (tp40) cc_final: 0.8267 (tp40) REVERT: C 1 MET cc_start: 0.8222 (tpt) cc_final: 0.7791 (tpt) REVERT: C 5 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8188 (mt) REVERT: C 6 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8338 (mtmt) REVERT: C 18 SER cc_start: 0.8412 (m) cc_final: 0.8033 (p) REVERT: C 53 GLU cc_start: 0.7462 (pt0) cc_final: 0.7209 (pt0) REVERT: C 109 ASP cc_start: 0.8292 (t70) cc_final: 0.8027 (t0) REVERT: C 169 LEU cc_start: 0.8666 (tp) cc_final: 0.8442 (tp) REVERT: C 241 ASP cc_start: 0.8523 (t0) cc_final: 0.8314 (t0) REVERT: C 246 GLU cc_start: 0.7884 (pt0) cc_final: 0.7588 (pt0) REVERT: C 264 ASP cc_start: 0.8082 (t70) cc_final: 0.7535 (t0) REVERT: C 268 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8339 (mttm) REVERT: C 275 GLU cc_start: 0.7794 (tt0) cc_final: 0.7444 (tt0) REVERT: C 288 GLU cc_start: 0.8104 (tt0) cc_final: 0.7826 (tt0) REVERT: C 316 GLU cc_start: 0.8160 (tp30) cc_final: 0.7863 (tp30) REVERT: D 62 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 68 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: D 72 GLU cc_start: 0.7718 (mp0) cc_final: 0.7315 (mp0) REVERT: D 93 LYS cc_start: 0.8229 (tppt) cc_final: 0.7942 (tppt) REVERT: D 190 GLU cc_start: 0.8131 (mp0) cc_final: 0.7726 (mp0) REVERT: D 215 MET cc_start: 0.8307 (mtp) cc_final: 0.8025 (mtt) REVERT: D 243 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: D 253 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 256 GLU cc_start: 0.8065 (tt0) cc_final: 0.7822 (tt0) REVERT: E 3 ASP cc_start: 0.8117 (p0) cc_final: 0.7902 (p0) REVERT: E 46 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8042 (mtp85) REVERT: E 48 GLN cc_start: 0.7783 (tt0) cc_final: 0.7542 (mt0) REVERT: E 140 GLN cc_start: 0.8454 (mp10) cc_final: 0.8003 (mp10) REVERT: E 173 LEU cc_start: 0.8553 (mp) cc_final: 0.8238 (mp) REVERT: E 182 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: E 183 SER cc_start: 0.8439 (t) cc_final: 0.8056 (m) REVERT: E 190 GLU cc_start: 0.7587 (mp0) cc_final: 0.7179 (mp0) REVERT: E 201 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7255 (mtp85) REVERT: E 205 TYR cc_start: 0.8004 (m-80) cc_final: 0.7304 (m-80) REVERT: E 232 ASN cc_start: 0.8588 (m-40) cc_final: 0.8244 (m110) REVERT: E 249 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7610 (mmpt) REVERT: E 253 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7195 (tm-30) REVERT: E 269 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7451 (mm-30) REVERT: E 287 GLN cc_start: 0.7522 (tp40) cc_final: 0.6894 (tp40) REVERT: E 288 GLU cc_start: 0.7528 (pt0) cc_final: 0.7178 (pt0) REVERT: E 290 ASN cc_start: 0.7568 (p0) cc_final: 0.7332 (p0) REVERT: E 291 ASP cc_start: 0.7282 (p0) cc_final: 0.6832 (p0) REVERT: F 1 MET cc_start: 0.8406 (tpp) cc_final: 0.8202 (tpp) REVERT: F 6 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7679 (mtpp) REVERT: F 18 SER cc_start: 0.8611 (m) cc_final: 0.7973 (p) REVERT: F 54 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7623 (mtmm) REVERT: F 59 SER cc_start: 0.8870 (m) cc_final: 0.7953 (p) REVERT: F 66 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7991 (mpt180) REVERT: F 97 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7214 (mt-10) REVERT: F 138 TYR cc_start: 0.8191 (t80) cc_final: 0.7886 (t80) REVERT: F 139 GLU cc_start: 0.7875 (mp0) cc_final: 0.7283 (mp0) REVERT: F 173 LEU cc_start: 0.8487 (tp) cc_final: 0.8271 (tt) REVERT: F 190 GLU cc_start: 0.7606 (mp0) cc_final: 0.7160 (mp0) REVERT: F 209 GLU cc_start: 0.8001 (tt0) cc_final: 0.7604 (tt0) REVERT: F 236 THR cc_start: 0.8878 (t) cc_final: 0.8507 (p) REVERT: F 249 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7925 (mtmt) REVERT: F 265 LEU cc_start: 0.8580 (mt) cc_final: 0.8350 (mp) REVERT: F 295 ASN cc_start: 0.8343 (t0) cc_final: 0.8084 (t0) REVERT: F 298 GLU cc_start: 0.8217 (mp0) cc_final: 0.7976 (mt-10) REVERT: F 317 PHE cc_start: 0.8792 (m-80) cc_final: 0.8530 (m-80) REVERT: G 8 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: G 54 LYS cc_start: 0.6728 (pttm) cc_final: 0.6467 (pttm) REVERT: G 72 GLU cc_start: 0.7740 (mp0) cc_final: 0.7166 (mp0) REVERT: G 113 TYR cc_start: 0.7585 (m-80) cc_final: 0.7305 (m-80) REVERT: G 162 MET cc_start: -0.1939 (tpp) cc_final: -0.2526 (tpp) REVERT: G 176 VAL cc_start: 0.7409 (t) cc_final: 0.6921 (m) REVERT: G 177 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7669 (p) REVERT: G 181 VAL cc_start: 0.8750 (t) cc_final: 0.8392 (p) REVERT: G 182 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7921 (mt-10) REVERT: G 194 TYR cc_start: 0.8576 (t80) cc_final: 0.8257 (t80) REVERT: G 198 ASN cc_start: 0.8152 (m-40) cc_final: 0.7782 (t0) REVERT: G 216 LYS cc_start: 0.8219 (tppt) cc_final: 0.7794 (tppt) REVERT: G 243 MET cc_start: 0.7495 (mtm) cc_final: 0.7277 (mtm) REVERT: G 256 GLU cc_start: 0.7449 (pp20) cc_final: 0.6981 (pp20) REVERT: G 268 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7637 (mtmt) REVERT: G 275 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7046 (mt-10) REVERT: G 288 GLU cc_start: 0.8192 (tp30) cc_final: 0.7877 (tp30) REVERT: G 295 ASN cc_start: 0.7477 (t0) cc_final: 0.7021 (t0) REVERT: H 24 ILE cc_start: 0.8922 (mt) cc_final: 0.8530 (tt) REVERT: H 29 GLU cc_start: 0.8258 (tp30) cc_final: 0.7996 (tp30) REVERT: H 39 TYR cc_start: 0.8819 (m-80) cc_final: 0.8456 (m-80) REVERT: H 180 TYR cc_start: 0.8711 (p90) cc_final: 0.8322 (p90) REVERT: I 26 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7612 (mt0) REVERT: I 84 ASN cc_start: 0.8000 (m-40) cc_final: 0.7500 (m-40) REVERT: I 158 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6924 (ttp80) REVERT: I 241 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7547 (mmmt) REVERT: I 273 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7689 (mmpt) REVERT: I 284 TYR cc_start: 0.7747 (m-80) cc_final: 0.7000 (m-80) REVERT: I 491 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: I 496 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7709 (ttm170) REVERT: I 512 GLN cc_start: 0.8062 (tp40) cc_final: 0.7673 (tm-30) REVERT: I 574 SER cc_start: 0.8520 (t) cc_final: 0.7983 (p) REVERT: I 600 TYR cc_start: 0.8730 (m-80) cc_final: 0.8501 (m-80) REVERT: I 620 TYR cc_start: 0.8167 (m-80) cc_final: 0.7287 (m-80) REVERT: I 631 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8145 (ttp-170) REVERT: I 639 MET cc_start: 0.7590 (mmp) cc_final: 0.7326 (mmp) REVERT: I 668 ASP cc_start: 0.7085 (p0) cc_final: 0.6800 (p0) REVERT: I 696 LEU cc_start: 0.8589 (mt) cc_final: 0.8370 (mm) REVERT: I 707 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8551 (mt) REVERT: I 746 VAL cc_start: 0.8688 (p) cc_final: 0.8436 (p) REVERT: I 750 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8650 (m) REVERT: I 754 ASN cc_start: 0.8647 (m-40) cc_final: 0.8315 (m-40) REVERT: I 772 LYS cc_start: 0.7651 (mptp) cc_final: 0.7266 (mptp) REVERT: I 776 GLN cc_start: 0.8137 (mp10) cc_final: 0.7632 (mm-40) REVERT: I 783 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7622 (tm-30) REVERT: I 802 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8258 (ttp80) REVERT: I 825 GLN cc_start: 0.8076 (tp40) cc_final: 0.7734 (tp40) REVERT: I 827 ASN cc_start: 0.8059 (t0) cc_final: 0.7696 (t0) REVERT: I 830 MET cc_start: 0.8065 (mtm) cc_final: 0.7729 (mtm) REVERT: I 833 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8367 (ttmm) REVERT: I 851 GLU cc_start: 0.8130 (tp30) cc_final: 0.7872 (tp30) REVERT: I 870 GLU cc_start: 0.7900 (tp30) cc_final: 0.7338 (tp30) REVERT: I 878 ASP cc_start: 0.8503 (t0) cc_final: 0.8063 (t0) REVERT: I 881 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7734 (pp20) REVERT: I 901 VAL cc_start: 0.8785 (t) cc_final: 0.8549 (p) REVERT: I 902 TYR cc_start: 0.8716 (p90) cc_final: 0.8511 (p90) REVERT: I 920 GLN cc_start: 0.8469 (mt0) cc_final: 0.8162 (mt0) REVERT: I 923 GLU cc_start: 0.7896 (pp20) cc_final: 0.7605 (pp20) REVERT: I 942 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8912 (mmmt) REVERT: J 22 GLU cc_start: 0.7647 (pt0) cc_final: 0.7132 (pm20) REVERT: J 58 GLN cc_start: 0.8301 (mt0) cc_final: 0.8050 (mt0) REVERT: J 88 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7188 (mtt180) REVERT: J 89 GLN cc_start: 0.8328 (mm110) cc_final: 0.8104 (mm110) REVERT: J 91 GLN cc_start: 0.8454 (mt0) cc_final: 0.8140 (mt0) REVERT: J 92 GLU cc_start: 0.8128 (tp30) cc_final: 0.7606 (tp30) REVERT: J 93 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8493 (tt) REVERT: J 120 GLN cc_start: 0.8382 (tp40) cc_final: 0.8040 (tt0) REVERT: J 143 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7384 (tp40) REVERT: K 13 GLU cc_start: 0.7110 (tt0) cc_final: 0.6908 (tt0) REVERT: K 22 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: K 41 GLU cc_start: 0.7061 (tp30) cc_final: 0.6444 (tp30) REVERT: K 52 GLU cc_start: 0.7803 (pp20) cc_final: 0.7219 (pp20) REVERT: K 71 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: K 94 GLU cc_start: 0.7730 (tp30) cc_final: 0.7170 (tp30) REVERT: K 131 GLU cc_start: 0.7492 (tp30) cc_final: 0.7007 (tp30) outliers start: 112 outliers final: 88 residues processed: 1020 average time/residue: 0.2162 time to fit residues: 337.4370 Evaluate side-chains 1072 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 966 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 501 GLN Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 821 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 940 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 211 optimal weight: 0.1980 chunk 272 optimal weight: 0.9990 chunk 265 optimal weight: 0.4980 chunk 210 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 279 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114049 restraints weight = 44021.211| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.85 r_work: 0.3332 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 29660 Z= 0.204 Angle : 0.785 59.199 40467 Z= 0.418 Chirality : 0.045 0.346 4565 Planarity : 0.004 0.058 4974 Dihedral : 15.200 179.957 4931 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.77 % Allowed : 23.46 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.30 (0.14), residues: 3399 helix: 1.34 (0.14), residues: 1445 sheet: -0.16 (0.23), residues: 436 loop : -0.79 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 68 TYR 0.022 0.002 TYR I 844 PHE 0.032 0.002 PHE E 151 TRP 0.031 0.002 TRP I 154 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00448 (29660) covalent geometry : angle 0.78506 (40467) hydrogen bonds : bond 0.03639 ( 1334) hydrogen bonds : angle 4.48048 ( 3811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10082.31 seconds wall clock time: 172 minutes 35.83 seconds (10355.83 seconds total)