Starting phenix.real_space_refine on Wed Jan 22 00:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461.map" model { file = "/net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d0t_46461/01_2025/9d0t_46461_neut.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.028 sd= 0.604 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 S 129 5.16 5 C 21427 2.51 5 N 5641 2.21 5 O 6404 1.98 5 H 33578 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67179 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3821 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain: "B" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3722 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain: "C" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3604 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3596 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "E" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3790 Classifications: {'peptide': 245} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 240} Chain breaks: 1 Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3614 Classifications: {'peptide': 234} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3777 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "I" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3072 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 3 Chain: "J" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2832 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "K" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain breaks: 1 Chain: "O" Number of atoms: 30998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1909, 30998 Classifications: {'peptide': 1909} Link IDs: {'PTRANS': 67, 'TRANS': 1841} Chain breaks: 2 Chain: "P" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1439 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Time building chain proxies: 22.10, per 1000 atoms: 0.33 Number of scatterers: 67179 At special positions: 0 Unit cell: (139.908, 143.112, 165.54, 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 129 16.00 O 6404 8.00 N 5641 7.00 C 21427 6.00 H 33578 1.00 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: 13.12 Conformation dependent library (CDL) restraints added in 4.2 seconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7984 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 22 sheets defined 55.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.671A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.502A pdb=" N SER A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.736A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.851A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.033A pdb=" N GLN A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.588A pdb=" N TYR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.506A pdb=" N THR B 60 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 61 " --> pdb=" O SER B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.703A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 219 through 222 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.539A pdb=" N GLU C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.652A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.582A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'D' and resid 20 through 28 removed outlier: 3.607A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.530A pdb=" N ARG D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.624A pdb=" N TYR D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.703A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.862A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.541A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 29 removed outlier: 3.553A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.940A pdb=" N GLY E 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.552A pdb=" N LEU E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 207 removed outlier: 4.073A pdb=" N VAL E 207 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 249 removed outlier: 3.533A pdb=" N GLU E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.860A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 180 removed outlier: 5.458A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 201 removed outlier: 3.768A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 21 through 33 removed outlier: 4.022A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.524A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.144A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 248 removed outlier: 4.366A pdb=" N GLN G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN G 248 " --> pdb=" O GLN G 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 17 removed outlier: 3.679A pdb=" N GLU I 17 " --> pdb=" O ASN I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.583A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 192 removed outlier: 3.782A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 removed outlier: 3.599A pdb=" N TYR J 96 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 4.186A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 90 Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.614A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER K 142 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'O' and resid 80 through 89 removed outlier: 4.279A pdb=" N GLU O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 104 Processing helix chain 'O' and resid 121 through 126 removed outlier: 3.902A pdb=" N LEU O 126 " --> pdb=" O GLU O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 153 Processing helix chain 'O' and resid 239 through 251 Processing helix chain 'O' and resid 256 through 271 removed outlier: 3.926A pdb=" N SER O 262 " --> pdb=" O ALA O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 291 removed outlier: 3.711A pdb=" N HIS O 283 " --> pdb=" O TYR O 279 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 308 Processing helix chain 'O' and resid 313 through 322 Processing helix chain 'O' and resid 328 through 332 Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 357 through 359 No H-bonds generated for 'chain 'O' and resid 357 through 359' Processing helix chain 'O' and resid 364 through 377 removed outlier: 4.651A pdb=" N VAL O 368 " --> pdb=" O GLU O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 379 through 381 No H-bonds generated for 'chain 'O' and resid 379 through 381' Processing helix chain 'O' and resid 382 through 394 Proline residue: O 388 - end of helix removed outlier: 3.710A pdb=" N VAL O 394 " --> pdb=" O VAL O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 406 Processing helix chain 'O' and resid 407 through 415 Processing helix chain 'O' and resid 421 through 444 removed outlier: 5.390A pdb=" N HIS O 427 " --> pdb=" O ALA O 423 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET O 428 " --> pdb=" O ILE O 424 " (cutoff:3.500A) Processing helix chain 'O' and resid 464 through 481 Processing helix chain 'O' and resid 487 through 497 Proline residue: O 494 - end of helix Processing helix chain 'O' and resid 504 through 523 removed outlier: 3.754A pdb=" N SER O 513 " --> pdb=" O GLU O 509 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR O 520 " --> pdb=" O LYS O 516 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE O 521 " --> pdb=" O ALA O 517 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS O 523 " --> pdb=" O GLU O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 557 Processing helix chain 'O' and resid 567 through 586 removed outlier: 4.940A pdb=" N ASN O 580 " --> pdb=" O GLU O 576 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE O 581 " --> pdb=" O ILE O 577 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 599 Processing helix chain 'O' and resid 599 through 607 removed outlier: 4.356A pdb=" N TYR O 603 " --> pdb=" O SER O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 612 through 628 Processing helix chain 'O' and resid 634 through 655 removed outlier: 3.566A pdb=" N LEU O 642 " --> pdb=" O ILE O 638 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL O 648 " --> pdb=" O GLN O 644 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG O 650 " --> pdb=" O THR O 646 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE O 651 " --> pdb=" O ARG O 647 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET O 654 " --> pdb=" O ARG O 650 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP O 655 " --> pdb=" O PHE O 651 " (cutoff:3.500A) Processing helix chain 'O' and resid 657 through 660 removed outlier: 4.034A pdb=" N VAL O 660 " --> pdb=" O LEU O 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 657 through 660' Processing helix chain 'O' and resid 661 through 672 Processing helix chain 'O' and resid 677 through 694 removed outlier: 3.785A pdb=" N PHE O 694 " --> pdb=" O SER O 690 " (cutoff:3.500A) Processing helix chain 'O' and resid 708 through 713 removed outlier: 3.547A pdb=" N ASP O 712 " --> pdb=" O SER O 708 " (cutoff:3.500A) Processing helix chain 'O' and resid 713 through 726 Processing helix chain 'O' and resid 736 through 746 Processing helix chain 'O' and resid 747 through 749 No H-bonds generated for 'chain 'O' and resid 747 through 749' Processing helix chain 'O' and resid 750 through 765 removed outlier: 3.604A pdb=" N MET O 754 " --> pdb=" O VAL O 750 " (cutoff:3.500A) Processing helix chain 'O' and resid 766 through 768 No H-bonds generated for 'chain 'O' and resid 766 through 768' Processing helix chain 'O' and resid 771 through 789 Processing helix chain 'O' and resid 790 through 807 removed outlier: 3.794A pdb=" N TYR O 796 " --> pdb=" O LYS O 792 " (cutoff:3.500A) Processing helix chain 'O' and resid 818 through 832 Proline residue: O 824 - end of helix Processing helix chain 'O' and resid 835 through 853 Processing helix chain 'O' and resid 865 through 867 No H-bonds generated for 'chain 'O' and resid 865 through 867' Processing helix chain 'O' and resid 868 through 884 Processing helix chain 'O' and resid 885 through 891 removed outlier: 3.772A pdb=" N GLU O 891 " --> pdb=" O SER O 888 " (cutoff:3.500A) Processing helix chain 'O' and resid 892 through 907 Processing helix chain 'O' and resid 909 through 929 removed outlier: 3.653A pdb=" N VAL O 914 " --> pdb=" O PRO O 910 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE O 915 " --> pdb=" O PRO O 911 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 918 " --> pdb=" O VAL O 914 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL O 919 " --> pdb=" O ILE O 915 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE O 920 " --> pdb=" O THR O 916 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS O 921 " --> pdb=" O SER O 917 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU O 927 " --> pdb=" O ALA O 923 " (cutoff:3.500A) Processing helix chain 'O' and resid 938 through 942 removed outlier: 4.386A pdb=" N ASP O 941 " --> pdb=" O PHE O 938 " (cutoff:3.500A) Processing helix chain 'O' and resid 956 through 960 removed outlier: 4.359A pdb=" N PHE O 960 " --> pdb=" O PRO O 957 " (cutoff:3.500A) Processing helix chain 'O' and resid 973 through 998 Processing helix chain 'O' and resid 1007 through 1024 Processing helix chain 'O' and resid 1025 through 1029 removed outlier: 4.246A pdb=" N LEU O1028 " --> pdb=" O GLY O1025 " (cutoff:3.500A) Processing helix chain 'O' and resid 1031 through 1037 removed outlier: 4.336A pdb=" N ASN O1035 " --> pdb=" O PRO O1032 " (cutoff:3.500A) Processing helix chain 'O' and resid 1166 through 1194 removed outlier: 3.791A pdb=" N LEU O1170 " --> pdb=" O ASN O1166 " (cutoff:3.500A) Processing helix chain 'O' and resid 1198 through 1214 Processing helix chain 'O' and resid 1230 through 1239 Processing helix chain 'O' and resid 1248 through 1266 Processing helix chain 'O' and resid 1276 through 1289 Processing helix chain 'O' and resid 1292 through 1310 Proline residue: O1298 - end of helix removed outlier: 3.586A pdb=" N GLN O1309 " --> pdb=" O HIS O1305 " (cutoff:3.500A) Processing helix chain 'O' and resid 1312 through 1331 removed outlier: 3.531A pdb=" N VAL O1316 " --> pdb=" O GLY O1312 " (cutoff:3.500A) Proline residue: O1323 - end of helix Processing helix chain 'O' and resid 1336 through 1345 Processing helix chain 'O' and resid 1346 through 1356 removed outlier: 3.766A pdb=" N LYS O1352 " --> pdb=" O LYS O1348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET O1354 " --> pdb=" O HIS O1350 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR O1355 " --> pdb=" O ARG O1351 " (cutoff:3.500A) Processing helix chain 'O' and resid 1359 through 1370 Processing helix chain 'O' and resid 1379 through 1390 Processing helix chain 'O' and resid 1403 through 1411 removed outlier: 4.579A pdb=" N LEU O1408 " --> pdb=" O GLN O1405 " (cutoff:3.500A) Proline residue: O1409 - end of helix Processing helix chain 'O' and resid 1415 through 1418 Processing helix chain 'O' and resid 1419 through 1453 removed outlier: 3.749A pdb=" N LYS O1431 " --> pdb=" O ALA O1427 " (cutoff:3.500A) Processing helix chain 'O' and resid 1459 through 1472 removed outlier: 3.976A pdb=" N PHE O1463 " --> pdb=" O LYS O1459 " (cutoff:3.500A) Processing helix chain 'O' and resid 1480 through 1489 Processing helix chain 'O' and resid 1490 through 1494 removed outlier: 3.503A pdb=" N LYS O1494 " --> pdb=" O ILE O1491 " (cutoff:3.500A) Processing helix chain 'O' and resid 1495 through 1519 Processing helix chain 'O' and resid 1522 through 1528 Processing helix chain 'O' and resid 1545 through 1554 removed outlier: 3.852A pdb=" N THR O1551 " --> pdb=" O PRO O1547 " (cutoff:3.500A) Processing helix chain 'O' and resid 1592 through 1606 removed outlier: 3.750A pdb=" N LEU O1605 " --> pdb=" O THR O1601 " (cutoff:3.500A) Processing helix chain 'O' and resid 1607 through 1622 Processing helix chain 'O' and resid 1629 through 1645 removed outlier: 3.536A pdb=" N VAL O1633 " --> pdb=" O SER O1629 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE O1636 " --> pdb=" O ASN O1632 " (cutoff:3.500A) Processing helix chain 'O' and resid 1651 through 1663 removed outlier: 4.289A pdb=" N LEU O1655 " --> pdb=" O ASN O1651 " (cutoff:3.500A) Processing helix chain 'O' and resid 1667 through 1684 Processing helix chain 'O' and resid 1685 through 1687 No H-bonds generated for 'chain 'O' and resid 1685 through 1687' Processing helix chain 'O' and resid 1689 through 1709 Processing helix chain 'O' and resid 1713 through 1727 Processing helix chain 'O' and resid 1732 through 1736 Processing helix chain 'O' and resid 1738 through 1745 Processing helix chain 'O' and resid 1758 through 1775 removed outlier: 4.207A pdb=" N SER O1762 " --> pdb=" O THR O1758 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS O1763 " --> pdb=" O HIS O1759 " (cutoff:3.500A) Processing helix chain 'O' and resid 1781 through 1788 removed outlier: 3.824A pdb=" N PHE O1785 " --> pdb=" O VAL O1781 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP O1786 " --> pdb=" O GLY O1782 " (cutoff:3.500A) Processing helix chain 'O' and resid 1795 through 1813 removed outlier: 3.640A pdb=" N GLN O1812 " --> pdb=" O LEU O1808 " (cutoff:3.500A) Processing helix chain 'O' and resid 1819 through 1829 Processing helix chain 'O' and resid 1842 through 1857 removed outlier: 3.564A pdb=" N ILE O1856 " --> pdb=" O GLN O1852 " (cutoff:3.500A) Processing helix chain 'O' and resid 1858 through 1863 removed outlier: 4.084A pdb=" N ASP O1861 " --> pdb=" O ASN O1858 " (cutoff:3.500A) Processing helix chain 'O' and resid 1867 through 1872 removed outlier: 3.521A pdb=" N ILE O1872 " --> pdb=" O PRO O1868 " (cutoff:3.500A) Processing helix chain 'O' and resid 1874 through 1891 Processing helix chain 'O' and resid 1892 through 1894 No H-bonds generated for 'chain 'O' and resid 1892 through 1894' Processing helix chain 'O' and resid 1895 through 1900 removed outlier: 3.587A pdb=" N LEU O1899 " --> pdb=" O ASN O1895 " (cutoff:3.500A) Processing helix chain 'O' and resid 1901 through 1903 No H-bonds generated for 'chain 'O' and resid 1901 through 1903' Processing helix chain 'O' and resid 1917 through 1924 removed outlier: 3.728A pdb=" N CYS O1921 " --> pdb=" O HIS O1917 " (cutoff:3.500A) Processing helix chain 'O' and resid 1927 through 1935 Processing helix chain 'O' and resid 1941 through 1952 removed outlier: 3.910A pdb=" N ALA O1946 " --> pdb=" O LYS O1942 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA O1947 " --> pdb=" O ASN O1943 " (cutoff:3.500A) Processing helix chain 'O' and resid 1963 through 1978 Processing helix chain 'O' and resid 1983 through 1997 Processing helix chain 'O' and resid 2004 through 2020 removed outlier: 3.593A pdb=" N VAL O2008 " --> pdb=" O VAL O2004 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP O2016 " --> pdb=" O SER O2012 " (cutoff:3.500A) Processing helix chain 'O' and resid 2023 through 2038 removed outlier: 4.190A pdb=" N LEU O2027 " --> pdb=" O GLU O2023 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY O2037 " --> pdb=" O ARG O2033 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU O2038 " --> pdb=" O PHE O2034 " (cutoff:3.500A) Processing helix chain 'O' and resid 2045 through 2050 Processing helix chain 'O' and resid 2051 through 2054 Processing helix chain 'O' and resid 2056 through 2071 Processing helix chain 'O' and resid 2080 through 2094 removed outlier: 3.698A pdb=" N SER O2091 " --> pdb=" O SER O2087 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP O2092 " --> pdb=" O ASN O2088 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG O2094 " --> pdb=" O SER O2090 " (cutoff:3.500A) Processing helix chain 'O' and resid 2097 through 2114 removed outlier: 3.756A pdb=" N ALA O2102 " --> pdb=" O MET O2098 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA O2103 " --> pdb=" O THR O2099 " (cutoff:3.500A) Processing helix chain 'O' and resid 2117 through 2122 Processing helix chain 'O' and resid 2123 through 2125 No H-bonds generated for 'chain 'O' and resid 2123 through 2125' Processing helix chain 'O' and resid 2128 through 2133 removed outlier: 4.235A pdb=" N ASP O2132 " --> pdb=" O GLU O2128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU O2133 " --> pdb=" O GLU O2129 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 2128 through 2133' Processing helix chain 'P' and resid 51 through 58 Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 78 through 95 removed outlier: 3.522A pdb=" N MET P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP P 95 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 112 Processing helix chain 'P' and resid 118 through 123 Processing helix chain 'P' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 4.652A pdb=" N VAL A 225 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 232 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 4.022A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.767A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.110A pdb=" N THR B 225 " --> pdb=" O TYR I 215 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY I 40 " --> pdb=" O PHE I 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.984A pdb=" N THR C 34 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.603A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 150 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 158 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 removed outlier: 5.768A pdb=" N CYS D 32 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.542A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.503A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.549A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER E 79 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA E 141 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 156 through 158 removed outlier: 3.818A pdb=" N TYR E 165 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.599A pdb=" N ILE F 215 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.502A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY F 141 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.230A pdb=" N ILE G 54 " --> pdb=" O ASP G 211 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP G 211 " --> pdb=" O ILE G 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 67 through 70 removed outlier: 4.387A pdb=" N GLY G 145 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.562A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER I 141 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 136 through 139 removed outlier: 6.714A pdb=" N ILE J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP J 26 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 13 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS J 20 " --> pdb=" O GLY J 17 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS J 25 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL J 186 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 43 through 46 removed outlier: 4.176A pdb=" N VAL J 49 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY J 123 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 130 through 133 removed outlier: 3.692A pdb=" N ASP K 185 " --> pdb=" O GLY K 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY K 188 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.842A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 1536 through 1540 1853 hydrogen bonds defined for protein. 5376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.25 Time building geometry restraints manager: 16.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 33527 1.04 - 1.23: 4037 1.23 - 1.43: 10538 1.43 - 1.63: 19530 1.63 - 1.83: 207 Bond restraints: 67839 Sorted by residual: bond pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CA PRO B 105 " pdb=" C PRO B 105 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.56e+01 bond pdb=" N LYS O1297 " pdb=" CA LYS O1297 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.51e+01 bond pdb=" CA ILE G 82 " pdb=" CB ILE G 82 " ideal model delta sigma weight residual 1.534 1.561 -0.026 6.80e-03 2.16e+04 1.48e+01 bond pdb=" N ILE I 70 " pdb=" CA ILE I 70 " ideal model delta sigma weight residual 1.459 1.503 -0.043 1.15e-02 7.56e+03 1.43e+01 ... (remaining 67834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 103129 2.50 - 5.01: 17918 5.01 - 7.51: 1583 7.51 - 10.01: 58 10.01 - 12.52: 8 Bond angle restraints: 122696 Sorted by residual: angle pdb=" N PRO O 910 " pdb=" CA PRO O 910 " pdb=" C PRO O 910 " ideal model delta sigma weight residual 110.70 118.54 -7.84 1.22e+00 6.72e-01 4.12e+01 angle pdb=" N ASP O1388 " pdb=" CA ASP O1388 " pdb=" C ASP O1388 " ideal model delta sigma weight residual 113.12 105.62 7.50 1.25e+00 6.40e-01 3.60e+01 angle pdb=" C ALA O1602 " pdb=" N GLY O1603 " pdb=" CA GLY O1603 " ideal model delta sigma weight residual 119.98 126.54 -6.56 1.11e+00 8.12e-01 3.49e+01 angle pdb=" C LEU G 81 " pdb=" N ILE G 82 " pdb=" CA ILE G 82 " ideal model delta sigma weight residual 120.24 123.88 -3.64 6.30e-01 2.52e+00 3.34e+01 angle pdb=" CA GLY B 79 " pdb=" C GLY B 79 " pdb=" O GLY B 79 " ideal model delta sigma weight residual 119.69 116.06 3.63 6.30e-01 2.52e+00 3.33e+01 ... (remaining 122691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 29018 17.93 - 35.87: 1793 35.87 - 53.80: 745 53.80 - 71.74: 234 71.74 - 89.67: 59 Dihedral angle restraints: 31849 sinusoidal: 17294 harmonic: 14555 Sorted by residual: dihedral pdb=" C GLN O2025 " pdb=" N GLN O2025 " pdb=" CA GLN O2025 " pdb=" CB GLN O2025 " ideal model delta harmonic sigma weight residual -122.60 -132.63 10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" N VAL O1900 " pdb=" C VAL O1900 " pdb=" CA VAL O1900 " pdb=" CB VAL O1900 " ideal model delta harmonic sigma weight residual 123.40 133.31 -9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA LEU C 211 " pdb=" C LEU C 211 " pdb=" N GLU C 212 " pdb=" CA GLU C 212 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 31846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2975 0.076 - 0.153: 1548 0.153 - 0.229: 564 0.229 - 0.306: 157 0.306 - 0.382: 19 Chirality restraints: 5263 Sorted by residual: chirality pdb=" CB THR O1020 " pdb=" CA THR O1020 " pdb=" OG1 THR O1020 " pdb=" CG2 THR O1020 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB THR G 124 " pdb=" CA THR G 124 " pdb=" OG1 THR G 124 " pdb=" CG2 THR G 124 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 5260 not shown) Planarity restraints: 9992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN O 318 " -0.096 2.00e-02 2.50e+03 4.24e-01 2.70e+03 pdb=" CG ASN O 318 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN O 318 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN O 318 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN O 318 " 0.725 2.00e-02 2.50e+03 pdb="HD22 ASN O 318 " -0.732 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 299 " 0.158 2.00e-02 2.50e+03 1.80e-01 4.88e+02 pdb=" CG ASN O 299 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN O 299 " -0.159 2.00e-02 2.50e+03 pdb=" ND2 ASN O 299 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN O 299 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN O 299 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 162 " -0.145 2.00e-02 2.50e+03 1.58e-01 3.76e+02 pdb=" CD GLN D 162 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN D 162 " 0.135 2.00e-02 2.50e+03 pdb=" NE2 GLN D 162 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN D 162 " 0.233 2.00e-02 2.50e+03 pdb="HE22 GLN D 162 " -0.238 2.00e-02 2.50e+03 ... (remaining 9989 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 4810 2.24 - 2.83: 139263 2.83 - 3.42: 188852 3.42 - 4.01: 246747 4.01 - 4.60: 373746 Nonbonded interactions: 953418 Sorted by model distance: nonbonded pdb=" OG SER O 417 " pdb="HH21 ARG O1941 " model vdw 1.648 2.450 nonbonded pdb="HH11 ARG C 50 " pdb=" O ASP C 209 " model vdw 1.648 2.450 nonbonded pdb=" HG SER O 78 " pdb="HH22 ARG O1145 " model vdw 1.680 2.100 nonbonded pdb=" H ASP F 203 " pdb=" H GLU F 204 " model vdw 1.717 2.100 nonbonded pdb=" HZ2 LYS F 62 " pdb=" O ALA O2143 " model vdw 1.723 2.450 ... (remaining 953413 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.900 Extract box with map and model: 1.870 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 114.190 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.014 0.059 34261 Z= 0.935 Angle : 1.891 11.207 46360 Z= 1.307 Chirality : 0.103 0.382 5263 Planarity : 0.011 0.113 5926 Dihedral : 13.692 89.672 12688 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.32 % Allowed : 7.59 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.11), residues: 4188 helix: -1.21 (0.09), residues: 2125 sheet: -1.08 (0.23), residues: 473 loop : -1.62 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.015 TRP B 179 HIS 0.031 0.001 HIS O1714 PHE 0.095 0.017 PHE O 470 TYR 0.115 0.015 TYR I 119 ARG 0.005 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 895 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7133 (mp0) REVERT: B 224 TYR cc_start: 0.7592 (p90) cc_final: 0.7189 (p90) REVERT: C 178 MET cc_start: 0.7690 (ptm) cc_final: 0.7440 (ptp) REVERT: C 181 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7497 (mtmm) REVERT: C 184 MET cc_start: 0.7760 (ptp) cc_final: 0.7498 (ptm) REVERT: C 191 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6953 (pt0) REVERT: C 224 GLU cc_start: 0.6957 (pm20) cc_final: 0.6286 (pp20) REVERT: C 228 LYS cc_start: 0.7401 (ttmm) cc_final: 0.7061 (tttp) REVERT: D 22 TYR cc_start: 0.6627 (m-80) cc_final: 0.6406 (m-80) REVERT: D 82 SER cc_start: 0.7305 (t) cc_final: 0.7028 (p) REVERT: D 110 THR cc_start: 0.8437 (m) cc_final: 0.8224 (p) REVERT: D 144 GLU cc_start: 0.8160 (tp30) cc_final: 0.7689 (tm-30) REVERT: D 182 LYS cc_start: 0.8617 (tttt) cc_final: 0.8348 (tppp) REVERT: E 64 ILE cc_start: 0.7954 (mp) cc_final: 0.7722 (pp) REVERT: E 182 GLU cc_start: 0.8101 (tp30) cc_final: 0.6923 (tp30) REVERT: F 41 ASN cc_start: 0.7545 (m-40) cc_final: 0.7085 (m110) REVERT: G 114 ASP cc_start: 0.8181 (t0) cc_final: 0.7967 (t0) REVERT: G 246 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7986 (tm-30) REVERT: J 7 ILE cc_start: 0.7216 (mt) cc_final: 0.7008 (tp) REVERT: J 104 PHE cc_start: 0.7464 (m-80) cc_final: 0.7065 (m-10) REVERT: J 139 SER cc_start: 0.8769 (m) cc_final: 0.8358 (p) REVERT: J 157 ASN cc_start: 0.8541 (m-40) cc_final: 0.8183 (m-40) REVERT: J 159 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7051 (mm-30) REVERT: J 161 GLU cc_start: 0.8252 (mp0) cc_final: 0.7957 (mp0) REVERT: J 186 VAL cc_start: 0.7069 (t) cc_final: 0.6845 (t) REVERT: J 197 LYS cc_start: 0.6582 (tttt) cc_final: 0.5890 (tmmt) REVERT: K 1 MET cc_start: 0.7106 (tpp) cc_final: 0.6669 (tpt) REVERT: K 81 SER cc_start: 0.8743 (t) cc_final: 0.8369 (p) REVERT: K 151 ASP cc_start: 0.7526 (p0) cc_final: 0.7148 (p0) REVERT: K 187 ASP cc_start: 0.8768 (m-30) cc_final: 0.8130 (t0) REVERT: O 383 MET cc_start: 0.7944 (tpp) cc_final: 0.7706 (tpt) REVERT: O 506 ARG cc_start: 0.6758 (mmm160) cc_final: 0.6427 (mtp180) REVERT: O 675 MET cc_start: 0.8488 (mpp) cc_final: 0.8050 (mpp) REVERT: O 695 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7500 (pt) REVERT: O 791 ASP cc_start: 0.8475 (m-30) cc_final: 0.8212 (m-30) REVERT: O 973 SER cc_start: 0.8834 (m) cc_final: 0.8501 (p) REVERT: O 1195 GLU cc_start: 0.8018 (pm20) cc_final: 0.7590 (pm20) REVERT: O 1275 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8408 (tppp) REVERT: O 1402 ILE cc_start: 0.8246 (mt) cc_final: 0.7930 (pp) REVERT: O 1518 ASP cc_start: 0.6393 (m-30) cc_final: 0.6108 (m-30) REVERT: O 1595 GLU cc_start: 0.7693 (mp0) cc_final: 0.6905 (mp0) REVERT: O 1652 MET cc_start: 0.8780 (mmm) cc_final: 0.6820 (mmm) REVERT: O 1653 SER cc_start: 0.8187 (p) cc_final: 0.6887 (m) REVERT: O 1811 ASN cc_start: 0.8510 (m-40) cc_final: 0.7974 (m110) REVERT: O 1843 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7351 (tm-30) REVERT: O 2109 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7844 (mt-10) REVERT: P 100 SER cc_start: 0.7636 (m) cc_final: 0.6753 (p) REVERT: P 120 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7219 (tp30) outliers start: 12 outliers final: 4 residues processed: 905 average time/residue: 2.9606 time to fit residues: 3168.5354 Evaluate side-chains 529 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain O residue 695 ILE Chi-restraints excluded: chain O residue 894 ASP Chi-restraints excluded: chain O residue 1759 HIS Chi-restraints excluded: chain O residue 1943 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 0.5980 chunk 316 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 213 optimal weight: 0.4980 chunk 169 optimal weight: 0.5980 chunk 327 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 379 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN C 177 GLN D 167 ASN D 244 GLN D 246 GLN E 180 GLN E 188 HIS F 43 HIS F 148 GLN G 121 GLN G 225 ASN G 244 GLN I 12 ASN I 86 GLN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 595 ASN O 611 ASN O 698 GLN O 764 GLN O 795 ASN O 963 GLN O 968 GLN O1171 GLN O1181 HIS O1244 ASN O1319 ASN O1342 ASN O1594 ASN O1760 GLN O1799 GLN O1895 ASN O2105 ASN P 92 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067304 restraints weight = 249892.966| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.95 r_work: 0.3034 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34261 Z= 0.208 Angle : 0.641 7.806 46360 Z= 0.345 Chirality : 0.042 0.168 5263 Planarity : 0.005 0.053 5926 Dihedral : 5.088 114.543 4587 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.18 % Allowed : 16.55 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4188 helix: 0.87 (0.11), residues: 2133 sheet: -0.48 (0.21), residues: 513 loop : -1.33 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 158 HIS 0.009 0.001 HIS I 115 PHE 0.017 0.002 PHE F 179 TYR 0.022 0.001 TYR O1296 ARG 0.010 0.001 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 525 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7815 (pp20) REVERT: C 178 MET cc_start: 0.8853 (ptm) cc_final: 0.8641 (ptp) REVERT: C 226 TYR cc_start: 0.8091 (t80) cc_final: 0.7763 (t80) REVERT: D 22 TYR cc_start: 0.8143 (m-80) cc_final: 0.7620 (m-10) REVERT: D 131 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8902 (m) REVERT: D 144 GLU cc_start: 0.8475 (tp30) cc_final: 0.7997 (tm-30) REVERT: D 183 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7817 (tm-30) REVERT: E 134 MET cc_start: 0.7042 (tpp) cc_final: 0.6819 (tpp) REVERT: E 195 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: F 188 GLU cc_start: 0.8619 (tp30) cc_final: 0.8263 (tp30) REVERT: F 195 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: G 6 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7041 (p) REVERT: G 18 ASP cc_start: 0.8340 (t0) cc_final: 0.8035 (t0) REVERT: G 114 ASP cc_start: 0.8601 (t0) cc_final: 0.8123 (t0) REVERT: G 157 TYR cc_start: 0.8689 (p90) cc_final: 0.8470 (p90) REVERT: I 20 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6732 (m-70) REVERT: I 93 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8685 (tm-30) REVERT: I 126 TYR cc_start: 0.7728 (m-10) cc_final: 0.7482 (m-10) REVERT: J 97 GLU cc_start: 0.7045 (pt0) cc_final: 0.6822 (pt0) REVERT: J 153 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (pt) REVERT: J 197 LYS cc_start: 0.8161 (tttt) cc_final: 0.7822 (tttt) REVERT: K 172 MET cc_start: 0.5813 (mpt) cc_final: 0.5390 (mtt) REVERT: O 346 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8499 (mtm-85) REVERT: O 659 ARG cc_start: 0.8702 (ptp-170) cc_final: 0.8430 (ptp-170) REVERT: O 695 ILE cc_start: 0.8240 (mt) cc_final: 0.7943 (pt) REVERT: O 737 ASP cc_start: 0.8757 (t0) cc_final: 0.8307 (t0) REVERT: O 1176 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: O 1195 GLU cc_start: 0.8182 (pm20) cc_final: 0.7917 (pm20) REVERT: O 1463 PHE cc_start: 0.7819 (t80) cc_final: 0.7604 (t80) REVERT: O 1470 GLN cc_start: 0.8071 (tp40) cc_final: 0.7757 (tm-30) REVERT: O 1593 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: O 1978 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: P 70 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: P 82 MET cc_start: 0.8644 (tmm) cc_final: 0.8326 (ptt) REVERT: P 108 ASP cc_start: 0.8503 (m-30) cc_final: 0.8277 (m-30) REVERT: P 120 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7697 (tp30) outliers start: 81 outliers final: 25 residues processed: 581 average time/residue: 2.9604 time to fit residues: 2035.4048 Evaluate side-chains 512 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 477 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain I residue 20 HIS Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 984 LEU Chi-restraints excluded: chain O residue 1268 SER Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1604 HIS Chi-restraints excluded: chain O residue 1759 HIS Chi-restraints excluded: chain O residue 1943 ASN Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 240 optimal weight: 1.9990 chunk 407 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 177 GLN D 209 ASN E 215 ASN G 204 HIS I 12 ASN I 86 GLN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN O 611 ASN O 644 GLN O1242 HIS O1267 HIS O1870 GLN O1972 GLN O1997 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.059705 restraints weight = 251869.711| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.86 r_work: 0.2858 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34261 Z= 0.316 Angle : 0.657 10.404 46360 Z= 0.355 Chirality : 0.044 0.247 5263 Planarity : 0.005 0.056 5926 Dihedral : 4.940 48.492 4583 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.88 % Allowed : 17.19 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4188 helix: 0.94 (0.11), residues: 2170 sheet: -0.32 (0.21), residues: 511 loop : -1.43 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 530 HIS 0.011 0.002 HIS O1742 PHE 0.027 0.002 PHE F 179 TYR 0.025 0.002 TYR O1296 ARG 0.007 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 500 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: C 178 MET cc_start: 0.8935 (ptm) cc_final: 0.8689 (ptp) REVERT: C 226 TYR cc_start: 0.8316 (t80) cc_final: 0.8046 (t80) REVERT: D 97 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7575 (ptm160) REVERT: D 183 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 235 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: E 118 ASP cc_start: 0.8158 (p0) cc_final: 0.7911 (p0) REVERT: E 134 MET cc_start: 0.7037 (tpp) cc_final: 0.6669 (tpp) REVERT: E 195 GLU cc_start: 0.8656 (tp30) cc_final: 0.8291 (tm-30) REVERT: G 20 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: G 114 ASP cc_start: 0.8649 (t0) cc_final: 0.8327 (t0) REVERT: G 157 TYR cc_start: 0.8768 (p90) cc_final: 0.8528 (p90) REVERT: I 93 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: J 113 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8672 (m110) REVERT: K 37 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7316 (tm-30) REVERT: K 71 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8242 (mm-30) REVERT: K 172 MET cc_start: 0.6660 (mpt) cc_final: 0.6230 (mtt) REVERT: O 346 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8593 (mtm-85) REVERT: O 695 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8088 (pt) REVERT: O 1470 GLN cc_start: 0.8442 (tp40) cc_final: 0.8065 (tm-30) REVERT: O 1497 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: O 1502 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8516 (t) REVERT: O 1593 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: O 1914 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (tt) REVERT: O 1978 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: P 70 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: P 82 MET cc_start: 0.8863 (tmm) cc_final: 0.8540 (ptm) outliers start: 107 outliers final: 35 residues processed: 580 average time/residue: 2.9177 time to fit residues: 2008.6142 Evaluate side-chains 485 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 437 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 179 PHE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 695 ILE Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 747 SER Chi-restraints excluded: chain O residue 815 ASP Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1590 ASN Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1604 HIS Chi-restraints excluded: chain O residue 1914 LEU Chi-restraints excluded: chain O residue 1943 ASN Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 329 optimal weight: 0.9980 chunk 403 optimal weight: 0.2980 chunk 180 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN E 180 GLN G 33 ASN I 20 HIS I 86 GLN I 143 HIS K 78 GLN O1193 ASN O1286 GLN ** O2088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.058021 restraints weight = 253072.040| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.84 r_work: 0.2817 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34261 Z= 0.305 Angle : 0.622 7.724 46360 Z= 0.334 Chirality : 0.042 0.176 5263 Planarity : 0.005 0.066 5926 Dihedral : 4.921 40.422 4581 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.07 % Allowed : 18.99 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4188 helix: 1.02 (0.11), residues: 2168 sheet: -0.29 (0.21), residues: 522 loop : -1.50 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 158 HIS 0.009 0.002 HIS O 539 PHE 0.021 0.002 PHE F 179 TYR 0.023 0.002 TYR O1296 ARG 0.007 0.001 ARG I 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 454 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: C 137 TYR cc_start: 0.8341 (m-80) cc_final: 0.8102 (m-80) REVERT: C 178 MET cc_start: 0.8934 (ptm) cc_final: 0.8687 (ptp) REVERT: C 184 MET cc_start: 0.8946 (ptp) cc_final: 0.8544 (ptm) REVERT: D 97 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7641 (ptm160) REVERT: D 107 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: D 183 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 134 MET cc_start: 0.6844 (tpp) cc_final: 0.6487 (tpp) REVERT: E 195 GLU cc_start: 0.8636 (tp30) cc_final: 0.8345 (tm-30) REVERT: E 206 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: F 188 GLU cc_start: 0.8852 (tp30) cc_final: 0.8531 (tp30) REVERT: G 20 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8055 (ptm160) REVERT: G 157 TYR cc_start: 0.8771 (p90) cc_final: 0.8497 (p90) REVERT: I 93 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: J 97 GLU cc_start: 0.7338 (pt0) cc_final: 0.7111 (pt0) REVERT: J 113 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8651 (m110) REVERT: J 145 GLN cc_start: 0.8867 (pm20) cc_final: 0.8522 (pm20) REVERT: J 171 LEU cc_start: 0.8179 (mm) cc_final: 0.7936 (tp) REVERT: K 37 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7363 (tm-30) REVERT: O 346 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: O 695 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8090 (pt) REVERT: O 737 ASP cc_start: 0.8848 (t0) cc_final: 0.8409 (t0) REVERT: O 889 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8914 (tp) REVERT: O 1458 TRP cc_start: 0.4892 (t60) cc_final: 0.4471 (t60) REVERT: O 1461 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6304 (tmm160) REVERT: O 1470 GLN cc_start: 0.8517 (tp40) cc_final: 0.8074 (tm-30) REVERT: O 1497 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: O 1502 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8534 (t) REVERT: O 1593 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: O 1914 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8733 (tt) REVERT: O 1978 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: P 70 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: P 90 ILE cc_start: 0.8511 (tt) cc_final: 0.8130 (mt) outliers start: 114 outliers final: 47 residues processed: 538 average time/residue: 3.0070 time to fit residues: 1922.6342 Evaluate side-chains 507 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 444 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 157 GLN Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 695 ILE Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 889 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 984 LEU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1461 ARG Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1517 SER Chi-restraints excluded: chain O residue 1589 LEU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1604 HIS Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1914 LEU Chi-restraints excluded: chain O residue 1943 ASN Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1961 SER Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 405 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN D 209 ASN I 86 GLN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 ASN K 78 GLN O1270 ASN O1286 GLN O2049 GLN O2088 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058743 restraints weight = 253109.238| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.83 r_work: 0.2836 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34261 Z= 0.207 Angle : 0.564 7.641 46360 Z= 0.300 Chirality : 0.040 0.185 5263 Planarity : 0.004 0.056 5926 Dihedral : 4.740 36.452 4581 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.42 % Allowed : 20.20 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4188 helix: 1.26 (0.11), residues: 2166 sheet: -0.19 (0.21), residues: 515 loop : -1.45 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 243 HIS 0.008 0.001 HIS I 115 PHE 0.018 0.001 PHE F 179 TYR 0.021 0.001 TYR O1296 ARG 0.004 0.000 ARG O1466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 462 time to evaluate : 4.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 TYR cc_start: 0.8288 (p90) cc_final: 0.7884 (p90) REVERT: C 109 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: C 137 TYR cc_start: 0.8361 (m-80) cc_final: 0.8091 (m-80) REVERT: C 178 MET cc_start: 0.8846 (ptm) cc_final: 0.8584 (ptp) REVERT: C 184 MET cc_start: 0.8903 (ptp) cc_final: 0.8410 (ptm) REVERT: C 195 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8220 (mptm) REVERT: C 211 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8150 (mt) REVERT: C 224 GLU cc_start: 0.7374 (pp20) cc_final: 0.7003 (pp20) REVERT: D 97 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7619 (ptm160) REVERT: D 107 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: D 183 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7772 (tm-30) REVERT: E 134 MET cc_start: 0.6930 (tpp) cc_final: 0.6571 (tpp) REVERT: E 150 ASP cc_start: 0.8112 (m-30) cc_final: 0.7850 (m-30) REVERT: E 195 GLU cc_start: 0.8587 (tp30) cc_final: 0.8267 (tm-30) REVERT: E 206 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: G 20 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8030 (ptm160) REVERT: G 157 TYR cc_start: 0.8757 (p90) cc_final: 0.8473 (p90) REVERT: I 93 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: I 203 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8285 (t0) REVERT: J 113 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8562 (m110) REVERT: J 171 LEU cc_start: 0.8220 (mm) cc_final: 0.7973 (tp) REVERT: K 37 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7410 (tm-30) REVERT: O 346 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8508 (mtm-85) REVERT: O 695 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8077 (pt) REVERT: O 737 ASP cc_start: 0.8830 (t0) cc_final: 0.8388 (t0) REVERT: O 889 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8876 (tp) REVERT: O 1195 GLU cc_start: 0.8321 (pm20) cc_final: 0.8008 (pm20) REVERT: O 1272 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8534 (mmmt) REVERT: O 1458 TRP cc_start: 0.4869 (t60) cc_final: 0.4452 (t60) REVERT: O 1470 GLN cc_start: 0.8442 (tp40) cc_final: 0.7983 (tm-30) REVERT: O 1497 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: O 1502 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8510 (t) REVERT: O 1593 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: O 1914 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8709 (tt) REVERT: O 1978 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: P 70 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: P 90 ILE cc_start: 0.8486 (tt) cc_final: 0.8125 (mt) outliers start: 90 outliers final: 44 residues processed: 529 average time/residue: 2.9075 time to fit residues: 1835.0695 Evaluate side-chains 506 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 444 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 695 ILE Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 889 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 984 LEU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1552 GLU Chi-restraints excluded: chain O residue 1589 LEU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1914 LEU Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 225 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 394 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN E 218 GLN I 86 GLN J 157 ASN K 78 GLN ** O 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1759 HIS O1811 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055695 restraints weight = 254147.758| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.81 r_work: 0.2761 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34261 Z= 0.398 Angle : 0.659 9.396 46360 Z= 0.355 Chirality : 0.044 0.214 5263 Planarity : 0.005 0.058 5926 Dihedral : 5.082 39.179 4579 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 3.12 % Allowed : 19.96 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4188 helix: 0.94 (0.11), residues: 2182 sheet: -0.24 (0.21), residues: 535 loop : -1.68 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 415 HIS 0.011 0.002 HIS P 106 PHE 0.027 0.002 PHE F 179 TYR 0.024 0.002 TYR O1296 ARG 0.008 0.001 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 451 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: C 137 TYR cc_start: 0.8413 (m-80) cc_final: 0.8175 (m-80) REVERT: C 178 MET cc_start: 0.8939 (ptm) cc_final: 0.8673 (ptp) REVERT: C 184 MET cc_start: 0.8855 (ptp) cc_final: 0.8351 (ptm) REVERT: C 211 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8275 (mt) REVERT: C 224 GLU cc_start: 0.7532 (pp20) cc_final: 0.7167 (pp20) REVERT: D 97 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7600 (ptm160) REVERT: D 107 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: D 183 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7652 (tm-30) REVERT: E 106 ASP cc_start: 0.8666 (p0) cc_final: 0.8311 (p0) REVERT: E 134 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6538 (tpp) REVERT: E 150 ASP cc_start: 0.8277 (m-30) cc_final: 0.8064 (m-30) REVERT: E 206 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: F 1 MET cc_start: 0.7945 (tpt) cc_final: 0.7499 (tpt) REVERT: G 20 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8171 (ptm160) REVERT: G 157 TYR cc_start: 0.8793 (p90) cc_final: 0.8513 (p90) REVERT: I 93 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: J 113 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8757 (t0) REVERT: J 145 GLN cc_start: 0.8878 (pm20) cc_final: 0.8613 (pm20) REVERT: J 171 LEU cc_start: 0.8272 (mm) cc_final: 0.8064 (tp) REVERT: K 169 GLU cc_start: 0.7512 (tt0) cc_final: 0.7012 (tm-30) REVERT: O 415 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: O 443 ILE cc_start: 0.9096 (mt) cc_final: 0.8806 (mp) REVERT: O 558 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7735 (mpp80) REVERT: O 737 ASP cc_start: 0.8880 (t0) cc_final: 0.8430 (t0) REVERT: O 889 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8919 (tp) REVERT: O 1007 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8709 (pp20) REVERT: O 1272 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8520 (mmmt) REVERT: O 1458 TRP cc_start: 0.4871 (t60) cc_final: 0.4555 (t60) REVERT: O 1470 GLN cc_start: 0.8562 (tp40) cc_final: 0.8082 (tm-30) REVERT: O 1497 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.9061 (mp0) REVERT: O 1502 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8565 (t) REVERT: O 1593 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: O 1747 ASP cc_start: 0.8191 (t0) cc_final: 0.7946 (t0) REVERT: O 1825 GLU cc_start: 0.8747 (tp30) cc_final: 0.8545 (tp30) REVERT: O 1978 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: P 70 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: P 90 ILE cc_start: 0.8547 (tt) cc_final: 0.8260 (mt) outliers start: 116 outliers final: 57 residues processed: 535 average time/residue: 3.1239 time to fit residues: 1981.8815 Evaluate side-chains 506 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 431 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 179 PHE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 558 ARG Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 747 SER Chi-restraints excluded: chain O residue 815 ASP Chi-restraints excluded: chain O residue 889 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 999 MET Chi-restraints excluded: chain O residue 1007 GLU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1466 ARG Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1604 HIS Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1943 ASN Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain O residue 2137 LEU Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 368 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 317 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN I 86 GLN K 41 HIS K 78 GLN O 633 ASN O1286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.063008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056422 restraints weight = 253308.310| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.81 r_work: 0.2780 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34261 Z= 0.271 Angle : 0.606 8.782 46360 Z= 0.323 Chirality : 0.041 0.159 5263 Planarity : 0.005 0.060 5926 Dihedral : 4.954 40.774 4579 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.91 % Allowed : 20.47 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4188 helix: 1.05 (0.11), residues: 2186 sheet: -0.14 (0.21), residues: 524 loop : -1.63 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 158 HIS 0.007 0.001 HIS O1173 PHE 0.020 0.002 PHE F 179 TYR 0.021 0.002 TYR O1296 ARG 0.007 0.001 ARG K 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 453 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: C 137 TYR cc_start: 0.8342 (m-80) cc_final: 0.8113 (m-80) REVERT: C 178 MET cc_start: 0.8867 (ptm) cc_final: 0.8600 (ptp) REVERT: C 211 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8232 (mt) REVERT: C 224 GLU cc_start: 0.7655 (pp20) cc_final: 0.7426 (pp20) REVERT: D 97 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7601 (ptm160) REVERT: D 107 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: D 183 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 106 ASP cc_start: 0.8686 (p0) cc_final: 0.8323 (p0) REVERT: E 134 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6910 (tpp) REVERT: E 138 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: E 150 ASP cc_start: 0.8305 (m-30) cc_final: 0.8079 (m-30) REVERT: E 206 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: F 1 MET cc_start: 0.8132 (tpt) cc_final: 0.7634 (tpt) REVERT: G 20 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8143 (ptm160) REVERT: G 157 TYR cc_start: 0.8768 (p90) cc_final: 0.8421 (p90) REVERT: G 178 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: I 93 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: J 97 GLU cc_start: 0.7420 (pt0) cc_final: 0.7139 (pt0) REVERT: J 145 GLN cc_start: 0.8847 (pm20) cc_final: 0.8520 (pm20) REVERT: K 169 GLU cc_start: 0.7432 (tt0) cc_final: 0.7172 (tm-30) REVERT: O 415 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: O 443 ILE cc_start: 0.9091 (mt) cc_final: 0.8800 (mp) REVERT: O 606 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: O 737 ASP cc_start: 0.8848 (t0) cc_final: 0.8397 (t0) REVERT: O 906 ASN cc_start: 0.8808 (m-40) cc_final: 0.8576 (m-40) REVERT: O 1007 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8649 (pp20) REVERT: O 1272 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8501 (mmmt) REVERT: O 1296 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8495 (p90) REVERT: O 1330 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8750 (tmmm) REVERT: O 1458 TRP cc_start: 0.4907 (t60) cc_final: 0.4672 (t60) REVERT: O 1470 GLN cc_start: 0.8512 (tp40) cc_final: 0.8144 (tm-30) REVERT: O 1497 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9044 (mp0) REVERT: O 1502 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8518 (t) REVERT: O 1593 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: O 1747 ASP cc_start: 0.8362 (t0) cc_final: 0.8078 (t0) REVERT: O 1978 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: P 70 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: P 90 ILE cc_start: 0.8510 (tt) cc_final: 0.8265 (mt) outliers start: 108 outliers final: 47 residues processed: 536 average time/residue: 3.0429 time to fit residues: 1940.4532 Evaluate side-chains 502 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 435 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 179 PHE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 606 GLU Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 953 LEU Chi-restraints excluded: chain O residue 984 LEU Chi-restraints excluded: chain O residue 999 MET Chi-restraints excluded: chain O residue 1007 GLU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1296 TYR Chi-restraints excluded: chain O residue 1330 LYS Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1466 ARG Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1517 SER Chi-restraints excluded: chain O residue 1552 GLU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1623 GLU Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain O residue 2137 LEU Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 265 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 399 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 335 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN I 86 GLN O 633 ASN O1286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.057047 restraints weight = 252588.434| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.80 r_work: 0.2796 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34261 Z= 0.227 Angle : 0.592 8.870 46360 Z= 0.314 Chirality : 0.040 0.158 5263 Planarity : 0.005 0.099 5926 Dihedral : 4.838 41.731 4579 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 2.58 % Allowed : 21.31 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 4188 helix: 1.20 (0.11), residues: 2180 sheet: -0.13 (0.21), residues: 519 loop : -1.57 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 243 HIS 0.007 0.001 HIS O1173 PHE 0.030 0.001 PHE K 46 TYR 0.020 0.001 TYR O1296 ARG 0.018 0.001 ARG O1828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 449 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: C 137 TYR cc_start: 0.8353 (m-80) cc_final: 0.8112 (m-80) REVERT: C 178 MET cc_start: 0.8792 (ptm) cc_final: 0.8529 (ptp) REVERT: C 211 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8260 (mt) REVERT: C 224 GLU cc_start: 0.7683 (pp20) cc_final: 0.7345 (pp20) REVERT: D 97 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7597 (ptm160) REVERT: D 107 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: D 183 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 106 ASP cc_start: 0.8686 (p0) cc_final: 0.8336 (p0) REVERT: E 138 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: E 150 ASP cc_start: 0.8337 (m-30) cc_final: 0.8121 (m-30) REVERT: E 206 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: F 1 MET cc_start: 0.8149 (tpt) cc_final: 0.7662 (tpt) REVERT: F 188 GLU cc_start: 0.8926 (tp30) cc_final: 0.8542 (tp30) REVERT: G 20 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8084 (ptm160) REVERT: G 157 TYR cc_start: 0.8762 (p90) cc_final: 0.8403 (p90) REVERT: G 178 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8590 (mtmm) REVERT: I 93 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: I 174 ASP cc_start: 0.7126 (t0) cc_final: 0.6788 (p0) REVERT: J 113 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (t0) REVERT: K 169 GLU cc_start: 0.7455 (tt0) cc_final: 0.7170 (tm-30) REVERT: O 415 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: O 443 ILE cc_start: 0.9094 (mt) cc_final: 0.8802 (mp) REVERT: O 504 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8734 (pttm) REVERT: O 558 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7722 (mpp80) REVERT: O 606 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: O 737 ASP cc_start: 0.8828 (t0) cc_final: 0.8376 (t0) REVERT: O 906 ASN cc_start: 0.8805 (m-40) cc_final: 0.8563 (m-40) REVERT: O 1007 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8665 (pp20) REVERT: O 1011 MET cc_start: 0.8827 (mtp) cc_final: 0.8557 (mtt) REVERT: O 1195 GLU cc_start: 0.8255 (pm20) cc_final: 0.7923 (pm20) REVERT: O 1272 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8499 (mmmt) REVERT: O 1296 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8475 (p90) REVERT: O 1330 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8771 (tmmm) REVERT: O 1470 GLN cc_start: 0.8465 (tp40) cc_final: 0.8101 (tm-30) REVERT: O 1497 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.9035 (mp0) REVERT: O 1593 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: O 1609 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8454 (mp0) REVERT: O 1747 ASP cc_start: 0.8296 (t0) cc_final: 0.8023 (t0) REVERT: O 1828 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7691 (mmm160) REVERT: O 1978 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: P 70 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: P 90 ILE cc_start: 0.8506 (tt) cc_final: 0.8262 (mt) outliers start: 96 outliers final: 44 residues processed: 527 average time/residue: 3.0253 time to fit residues: 1888.6123 Evaluate side-chains 502 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 437 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 179 PHE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 124 PHE Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 504 LYS Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 558 ARG Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 606 GLU Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 1007 GLU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1296 TYR Chi-restraints excluded: chain O residue 1330 LYS Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1466 ARG Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1517 SER Chi-restraints excluded: chain O residue 1552 GLU Chi-restraints excluded: chain O residue 1589 LEU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1623 GLU Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain O residue 2137 LEU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 310 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN E 154 GLN I 20 HIS I 86 GLN ** O 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 633 ASN O1171 GLN O1286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.054789 restraints weight = 255236.128| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.80 r_work: 0.2739 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 34261 Z= 0.377 Angle : 0.673 9.542 46360 Z= 0.360 Chirality : 0.044 0.163 5263 Planarity : 0.005 0.077 5926 Dihedral : 5.127 43.857 4579 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 2.72 % Allowed : 21.60 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4188 helix: 0.93 (0.11), residues: 2174 sheet: -0.14 (0.21), residues: 527 loop : -1.74 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 415 HIS 0.011 0.002 HIS O 846 PHE 0.027 0.002 PHE F 179 TYR 0.023 0.002 TYR O1296 ARG 0.011 0.001 ARG O1828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 445 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7836 (mp0) cc_final: 0.7551 (mp0) REVERT: C 109 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: C 137 TYR cc_start: 0.8395 (m-80) cc_final: 0.8145 (m-80) REVERT: C 178 MET cc_start: 0.8880 (ptm) cc_final: 0.8612 (ptp) REVERT: C 184 MET cc_start: 0.8762 (ptp) cc_final: 0.8368 (ptm) REVERT: C 211 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 107 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: D 183 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 106 ASP cc_start: 0.8782 (p0) cc_final: 0.8430 (p0) REVERT: E 138 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: E 150 ASP cc_start: 0.8379 (m-30) cc_final: 0.8147 (m-30) REVERT: E 206 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: F 188 GLU cc_start: 0.8978 (tp30) cc_final: 0.8766 (tp30) REVERT: G 20 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8142 (ptm160) REVERT: G 157 TYR cc_start: 0.8790 (p90) cc_final: 0.8439 (p90) REVERT: I 18 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7762 (t0) REVERT: I 93 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: I 174 ASP cc_start: 0.7234 (t0) cc_final: 0.6921 (p0) REVERT: J 113 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (t0) REVERT: J 145 GLN cc_start: 0.8898 (pm20) cc_final: 0.8602 (pm20) REVERT: K 169 GLU cc_start: 0.7549 (tt0) cc_final: 0.7293 (tm-30) REVERT: O 415 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7791 (m-10) REVERT: O 443 ILE cc_start: 0.9109 (mt) cc_final: 0.8793 (mp) REVERT: O 558 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7790 (mpp80) REVERT: O 654 MET cc_start: 0.9303 (mmm) cc_final: 0.8750 (mmt) REVERT: O 737 ASP cc_start: 0.8894 (t0) cc_final: 0.8439 (t0) REVERT: O 906 ASN cc_start: 0.8871 (m-40) cc_final: 0.8620 (m-40) REVERT: O 1007 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8776 (pp20) REVERT: O 1296 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8522 (p90) REVERT: O 1330 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8776 (tmmm) REVERT: O 1470 GLN cc_start: 0.8545 (tp40) cc_final: 0.8259 (tm-30) REVERT: O 1497 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9057 (mp0) REVERT: O 1502 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8546 (t) REVERT: O 1593 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: O 1609 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8515 (mp0) REVERT: O 1747 ASP cc_start: 0.8488 (t0) cc_final: 0.8187 (t0) REVERT: O 1828 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7846 (mmm160) REVERT: O 1978 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: O 2052 SER cc_start: 0.7119 (m) cc_final: 0.6875 (p) REVERT: P 70 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8248 (mp0) outliers start: 101 outliers final: 50 residues processed: 524 average time/residue: 3.0373 time to fit residues: 1887.1157 Evaluate side-chains 498 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 179 PHE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 195 GLN Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 124 PHE Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 425 ASP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 558 ARG Chi-restraints excluded: chain O residue 568 SER Chi-restraints excluded: chain O residue 726 CYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 1007 GLU Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1296 TYR Chi-restraints excluded: chain O residue 1330 LYS Chi-restraints excluded: chain O residue 1340 ILE Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1437 SER Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1466 ARG Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1502 VAL Chi-restraints excluded: chain O residue 1517 SER Chi-restraints excluded: chain O residue 1552 GLU Chi-restraints excluded: chain O residue 1589 LEU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1623 GLU Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1786 ASP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1953 CYS Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain O residue 1984 GLU Chi-restraints excluded: chain O residue 2053 LYS Chi-restraints excluded: chain O residue 2137 LEU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 392 optimal weight: 1.9990 chunk 407 optimal weight: 0.8980 chunk 355 optimal weight: 0.9980 chunk 227 optimal weight: 0.0980 chunk 272 optimal weight: 0.3980 chunk 246 optimal weight: 0.9980 chunk 252 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 225 optimal weight: 0.2980 chunk 338 optimal weight: 0.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN I 10 GLN I 86 GLN O 448 HIS O 633 ASN O1286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057821 restraints weight = 252226.131| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.80 r_work: 0.2815 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34261 Z= 0.174 Angle : 0.585 8.460 46360 Z= 0.307 Chirality : 0.040 0.152 5263 Planarity : 0.005 0.083 5926 Dihedral : 4.761 43.472 4579 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 1.64 % Allowed : 22.76 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 4188 helix: 1.29 (0.11), residues: 2171 sheet: -0.03 (0.21), residues: 518 loop : -1.55 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 243 HIS 0.006 0.001 HIS I 115 PHE 0.022 0.001 PHE K 46 TYR 0.018 0.001 TYR O1296 ARG 0.013 0.001 ARG O1828 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 439 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7803 (mp0) cc_final: 0.7557 (mp0) REVERT: C 109 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: C 137 TYR cc_start: 0.8290 (m-80) cc_final: 0.8019 (m-80) REVERT: C 184 MET cc_start: 0.8721 (ptp) cc_final: 0.8353 (ptm) REVERT: C 211 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8223 (mt) REVERT: C 224 GLU cc_start: 0.7717 (pp20) cc_final: 0.7509 (pp20) REVERT: D 183 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 106 ASP cc_start: 0.8761 (p0) cc_final: 0.8404 (p0) REVERT: E 138 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: E 150 ASP cc_start: 0.8396 (m-30) cc_final: 0.8175 (m-30) REVERT: E 206 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: E 208 MET cc_start: 0.8038 (mmm) cc_final: 0.7796 (mtt) REVERT: F 1 MET cc_start: 0.8204 (tpt) cc_final: 0.7977 (tpt) REVERT: G 114 ASP cc_start: 0.8729 (t0) cc_final: 0.8384 (t0) REVERT: G 157 TYR cc_start: 0.8737 (p90) cc_final: 0.8323 (p90) REVERT: G 178 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8653 (mtmm) REVERT: I 174 ASP cc_start: 0.7037 (t0) cc_final: 0.6729 (p0) REVERT: O 415 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7699 (m-10) REVERT: O 443 ILE cc_start: 0.9031 (mt) cc_final: 0.8744 (mp) REVERT: O 654 MET cc_start: 0.9302 (mmm) cc_final: 0.8769 (mmt) REVERT: O 737 ASP cc_start: 0.8824 (t0) cc_final: 0.8368 (t0) REVERT: O 906 ASN cc_start: 0.8787 (m-40) cc_final: 0.8481 (m-40) REVERT: O 1011 MET cc_start: 0.8783 (mtp) cc_final: 0.8510 (mtt) REVERT: O 1272 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8503 (mmmt) REVERT: O 1470 GLN cc_start: 0.8412 (tp40) cc_final: 0.8144 (tm-30) REVERT: O 1497 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.9012 (mp0) REVERT: O 1593 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: O 1609 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8461 (mp0) REVERT: O 1747 ASP cc_start: 0.8425 (t0) cc_final: 0.8141 (t0) REVERT: O 1828 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.7759 (mmm160) REVERT: O 1978 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: P 70 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8165 (mp0) outliers start: 61 outliers final: 28 residues processed: 487 average time/residue: 3.0768 time to fit residues: 1771.3520 Evaluate side-chains 467 residues out of total 3717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 429 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 415 TRP Chi-restraints excluded: chain O residue 532 LYS Chi-restraints excluded: chain O residue 739 LEU Chi-restraints excluded: chain O residue 926 THR Chi-restraints excluded: chain O residue 1291 LEU Chi-restraints excluded: chain O residue 1394 LYS Chi-restraints excluded: chain O residue 1400 CYS Chi-restraints excluded: chain O residue 1402 ILE Chi-restraints excluded: chain O residue 1463 PHE Chi-restraints excluded: chain O residue 1466 ARG Chi-restraints excluded: chain O residue 1497 GLU Chi-restraints excluded: chain O residue 1589 LEU Chi-restraints excluded: chain O residue 1593 GLU Chi-restraints excluded: chain O residue 1623 GLU Chi-restraints excluded: chain O residue 1725 TRP Chi-restraints excluded: chain O residue 1859 LEU Chi-restraints excluded: chain O residue 1978 GLU Chi-restraints excluded: chain O residue 2137 LEU Chi-restraints excluded: chain P residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 126 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 150 optimal weight: 0.0870 chunk 399 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 197 optimal weight: 0.0060 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 177 GLN I 86 GLN O 448 HIS O 633 ASN O1286 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.057041 restraints weight = 253131.206| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.79 r_work: 0.2796 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34261 Z= 0.227 Angle : 0.601 9.420 46360 Z= 0.316 Chirality : 0.040 0.156 5263 Planarity : 0.005 0.080 5926 Dihedral : 4.763 43.656 4579 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 1.43 % Allowed : 23.27 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.13), residues: 4188 helix: 1.33 (0.11), residues: 2172 sheet: -0.00 (0.21), residues: 511 loop : -1.54 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 243 HIS 0.007 0.001 HIS O1173 PHE 0.020 0.001 PHE K 46 TYR 0.020 0.001 TYR O1296 ARG 0.011 0.001 ARG O1828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37401.99 seconds wall clock time: 637 minutes 34.22 seconds (38254.22 seconds total)