Starting phenix.real_space_refine on Wed Nov 19 19:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616.map" model { file = "/net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6agb_9616/11_2025/6agb_9616_neut.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 369 5.49 5 S 99 5.16 5 C 15766 2.51 5 N 4818 2.21 5 O 6137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 7861 Classifications: {'RNA': 369} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 22, 'rna3p_pur': 159, 'rna3p_pyr': 159} Link IDs: {'rna2p': 51, 'rna3p': 317} Chain: "B" Number of atoms: 6389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6389 Classifications: {'peptide': 784} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 748} Chain breaks: 4 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1435 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "D" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1886 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1272 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1024 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26766 SG CYS K 90 69.956 73.033 54.491 1.00 75.51 S ATOM 26963 SG CYS K 115 68.220 69.065 50.918 1.00 93.76 S ATOM 26973 SG CYS K 117 66.648 69.615 54.531 1.00 94.53 S Time building chain proxies: 6.86, per 1000 atoms: 0.25 Number of scatterers: 27190 At special positions: 0 Unit cell: (153.12, 121.44, 208.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 369 15.00 O 6137 8.00 N 4818 7.00 C 15766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 862.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 115 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 117 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 42.6% alpha, 16.8% beta 84 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'B' and resid 58 through 85 removed outlier: 3.652A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.890A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.800A pdb=" N SER B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 145 through 166 removed outlier: 3.875A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.529A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.802A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.507A pdb=" N ARG B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 307 through 318 removed outlier: 4.473A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.663A pdb=" N GLU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.986A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 469 " --> pdb=" O GLN B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.663A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.567A pdb=" N ILE B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.803A pdb=" N ARG B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.658A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.793A pdb=" N TYR B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.847A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 4.014A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.722A pdb=" N GLN B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 40 through 57 removed outlier: 4.155A pdb=" N GLN C 45 " --> pdb=" O PRO C 41 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.646A pdb=" N LEU C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.529A pdb=" N CYS C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.917A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.914A pdb=" N ASP D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.632A pdb=" N ASN D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.665A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.642A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 4.012A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.958A pdb=" N MET D 273 " --> pdb=" O CYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 147 removed outlier: 3.915A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.911A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.648A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.851A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.541A pdb=" N ASN F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.543A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 83 removed outlier: 3.866A pdb=" N GLN G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 removed outlier: 3.651A pdb=" N ASP H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.550A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 4.161A pdb=" N SER H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.807A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 removed outlier: 3.702A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 76 removed outlier: 4.461A pdb=" N LEU I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.694A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.643A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.742A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.746A pdb=" N LEU I 164 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 165' Processing helix chain 'I' and resid 167 through 185 removed outlier: 4.335A pdb=" N ARG I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 4.177A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 4.540A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 36 removed outlier: 3.588A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 3.982A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 4.032A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.746A pdb=" N LEU J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.703A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.537A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 4.079A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.660A pdb=" N GLU J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 201' Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 227 Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.702A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.985A pdb=" N ALA K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 3.849A pdb=" N ALA K 63 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.549A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.038A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 393 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.847A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.672A pdb=" N VAL B 546 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 400 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.835A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 837 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 828 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 839 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER B 826 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 856 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.001A pdb=" N THR K 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C 17 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.950A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 78 removed outlier: 3.559A pdb=" N GLN E 73 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.540A pdb=" N ILE G 33 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N MET G 68 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.809A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR H 11 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU H 102 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS H 13 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.605A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE I 45 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE I 87 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 47 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.313A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 102 through 105 removed outlier: 3.528A pdb=" N LYS K 102 " --> pdb=" O MET K 114 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 219 hydrogen bonds 422 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5628 1.33 - 1.45: 8247 1.45 - 1.58: 13706 1.58 - 1.70: 737 1.70 - 1.82: 150 Bond restraints: 28468 Sorted by residual: bond pdb=" C ILE C 108 " pdb=" N PRO C 109 " ideal model delta sigma weight residual 1.337 1.388 -0.051 1.11e-02 8.12e+03 2.13e+01 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C PRO K 24 " pdb=" N PRO K 25 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.45e+00 bond pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.34e+00 bond pdb=" C ASP C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.24e+00 ... (remaining 28463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 39458 2.52 - 5.05: 651 5.05 - 7.57: 99 7.57 - 10.09: 15 10.09 - 12.61: 5 Bond angle restraints: 40228 Sorted by residual: angle pdb=" N ILE I 112 " pdb=" CA ILE I 112 " pdb=" C ILE I 112 " ideal model delta sigma weight residual 113.10 105.97 7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" C VAL B 361 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" N ASN D 215 " pdb=" CA ASN D 215 " pdb=" C ASN D 215 " ideal model delta sigma weight residual 111.14 106.00 5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N VAL H 111 " pdb=" CA VAL H 111 " pdb=" C VAL H 111 " ideal model delta sigma weight residual 108.82 103.02 5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 120.20 127.25 -7.05 1.50e+00 4.44e-01 2.21e+01 ... (remaining 40223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 16809 34.97 - 69.93: 965 69.93 - 104.90: 114 104.90 - 139.87: 2 139.87 - 174.84: 9 Dihedral angle restraints: 17899 sinusoidal: 10844 harmonic: 7055 Sorted by residual: dihedral pdb=" C4' A A 191 " pdb=" C3' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 35.90 -70.90 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " pdb=" C3' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 33.56 -68.56 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 200.00 43.12 156.88 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 17896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4422 0.076 - 0.152: 383 0.152 - 0.227: 43 0.227 - 0.303: 2 0.303 - 0.379: 2 Chirality restraints: 4852 Sorted by residual: chirality pdb=" C3' A A 367 " pdb=" C4' A A 367 " pdb=" O3' A A 367 " pdb=" C2' A A 367 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C3' G A 179 " pdb=" C4' G A 179 " pdb=" O3' G A 179 " pdb=" C2' G A 179 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' U A 266 " pdb=" C4' U A 266 " pdb=" O3' U A 266 " pdb=" C2' U A 266 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4849 not shown) Planarity restraints: 3725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 728 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO B 729 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 44 " 0.018 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP C 44 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP C 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 44 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 44 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 44 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 44 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 543 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO B 544 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 544 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 544 " -0.038 5.00e-02 4.00e+02 ... (remaining 3722 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 93 2.48 - 3.09: 15839 3.09 - 3.69: 42272 3.69 - 4.30: 61659 4.30 - 4.90: 93355 Nonbonded interactions: 213218 Sorted by model distance: nonbonded pdb=" O2' A A 191 " pdb=" OP1 C A 192 " model vdw 1.877 3.040 nonbonded pdb=" O2' C A 151 " pdb=" OP1 U A 190 " model vdw 1.911 3.040 nonbonded pdb=" O2' G A 96 " pdb=" O2 U A 158 " model vdw 2.251 3.040 nonbonded pdb=" O LEU J 238 " pdb=" OG SER J 242 " model vdw 2.266 3.040 nonbonded pdb=" O2' U A 363 " pdb=" O CYS D 222 " model vdw 2.272 3.040 ... (remaining 213213 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=0.40 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 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 : 0.007 0.614 28471 Z= 0.279 Angle : 0.838 12.614 40228 Z= 0.487 Chirality : 0.044 0.379 4852 Planarity : 0.006 0.078 3725 Dihedral : 18.493 174.837 13315 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.18 % Allowed : 3.20 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.14), residues: 2372 helix: -2.63 (0.12), residues: 896 sheet: -0.72 (0.24), residues: 426 loop : -2.70 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 113 TYR 0.029 0.002 TYR B 597 PHE 0.030 0.002 PHE K 34 TRP 0.049 0.003 TRP C 44 HIS 0.006 0.001 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.00333 (28468) covalent geometry : angle 0.83782 (40228) hydrogen bonds : bond 0.16521 ( 1006) hydrogen bonds : angle 6.94372 ( 2726) metal coordination : bond 0.57345 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 926 time to evaluate : 0.853 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: B 79 ASN cc_start: 0.7554 (t160) cc_final: 0.7334 (t0) REVERT: B 146 GLN cc_start: 0.8079 (pt0) cc_final: 0.7530 (pt0) REVERT: B 217 VAL cc_start: 0.7608 (t) cc_final: 0.7302 (m) REVERT: B 311 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6899 (mmtt) REVERT: B 342 ASN cc_start: 0.7845 (t0) cc_final: 0.7634 (t0) REVERT: B 452 ASP cc_start: 0.7214 (t0) cc_final: 0.5147 (t70) REVERT: B 588 GLN cc_start: 0.8278 (tt0) cc_final: 0.7956 (tt0) REVERT: C 19 TYR cc_start: 0.8022 (m-80) cc_final: 0.7685 (m-10) REVERT: C 91 LEU cc_start: 0.8290 (tp) cc_final: 0.8059 (tp) REVERT: C 97 ASP cc_start: 0.7371 (t0) cc_final: 0.6370 (t70) REVERT: C 103 VAL cc_start: 0.7941 (t) cc_final: 0.7669 (t) REVERT: C 118 THR cc_start: 0.6400 (m) cc_final: 0.6158 (m) REVERT: D 199 ILE cc_start: 0.8045 (mp) cc_final: 0.7776 (mt) REVERT: E 57 SER cc_start: 0.7418 (m) cc_final: 0.7014 (p) REVERT: G 41 TYR cc_start: 0.8703 (t80) cc_final: 0.8368 (t80) REVERT: G 76 LEU cc_start: 0.8774 (mt) cc_final: 0.8102 (mp) REVERT: G 98 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7080 (tp30) REVERT: H 39 ASN cc_start: 0.8017 (m110) cc_final: 0.7663 (m-40) REVERT: H 55 TYR cc_start: 0.7847 (p90) cc_final: 0.7645 (p90) REVERT: H 120 LYS cc_start: 0.7962 (tttt) cc_final: 0.7585 (tptp) REVERT: I 157 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7132 (tm-30) REVERT: I 159 VAL cc_start: 0.9195 (t) cc_final: 0.8872 (t) REVERT: J 191 ILE cc_start: 0.9206 (pt) cc_final: 0.8986 (pt) REVERT: K 134 TYR cc_start: 0.8083 (t80) cc_final: 0.7763 (t80) outliers start: 4 outliers final: 0 residues processed: 929 average time/residue: 0.2294 time to fit residues: 316.1184 Evaluate side-chains 492 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 90 GLN B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 251 HIS B 259 GLN B 266 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 463 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 505 ASN B 642 HIS B 665 GLN B 675 GLN B 677 ASN B 704 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 40 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 197 GLN E 50 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 37 ASN F 54 ASN F 76 GLN F 87 HIS G 28 GLN G 58 GLN H 40 ASN I 12 ASN I 34 HIS I 49 HIS I 143 HIS I 151 ASN I 172 GLN I 203 ASN J 95 GLN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 42 GLN K 94 HIS K 140 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.154429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121858 restraints weight = 51535.274| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.37 r_work: 0.3473 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28471 Z= 0.272 Angle : 0.780 14.051 40228 Z= 0.401 Chirality : 0.042 0.302 4852 Planarity : 0.006 0.076 3725 Dihedral : 21.010 173.474 8400 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 3.97 % Allowed : 14.44 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.16), residues: 2372 helix: -0.65 (0.16), residues: 929 sheet: -0.64 (0.24), residues: 461 loop : -2.02 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 780 TYR 0.023 0.003 TYR D 150 PHE 0.031 0.003 PHE B 657 TRP 0.021 0.002 TRP B 256 HIS 0.012 0.002 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00565 (28468) covalent geometry : angle 0.77958 (40228) hydrogen bonds : bond 0.05479 ( 1006) hydrogen bonds : angle 4.69244 ( 2726) metal coordination : bond 0.01623 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 564 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8316 (t0) cc_final: 0.7662 (t0) REVERT: B 201 ASN cc_start: 0.7287 (t0) cc_final: 0.7029 (t0) REVERT: B 225 LYS cc_start: 0.7414 (mtmt) cc_final: 0.6977 (mtmt) REVERT: B 255 ARG cc_start: 0.7663 (ttt180) cc_final: 0.7262 (ttp80) REVERT: B 311 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7470 (mmtt) REVERT: B 370 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7416 (pt) REVERT: B 461 LYS cc_start: 0.8275 (tptp) cc_final: 0.7896 (ttmm) REVERT: B 463 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6270 (m-40) REVERT: B 543 ILE cc_start: 0.9129 (pt) cc_final: 0.8891 (pt) REVERT: B 557 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9066 (tt) REVERT: B 632 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.6893 (pmt100) REVERT: B 650 SER cc_start: 0.7163 (p) cc_final: 0.6893 (p) REVERT: B 665 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: B 756 THR cc_start: 0.6878 (OUTLIER) cc_final: 0.6583 (t) REVERT: B 757 PHE cc_start: 0.7072 (t80) cc_final: 0.6829 (t80) REVERT: B 819 ASP cc_start: 0.7999 (m-30) cc_final: 0.7796 (m-30) REVERT: C 28 THR cc_start: 0.9157 (m) cc_final: 0.8861 (p) REVERT: C 33 MET cc_start: 0.6346 (mmm) cc_final: 0.6053 (mmt) REVERT: C 43 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5579 (pt) REVERT: C 47 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7064 (tp) REVERT: C 70 THR cc_start: 0.8308 (p) cc_final: 0.7507 (m) REVERT: C 123 GLN cc_start: 0.6509 (tm-30) cc_final: 0.5942 (tp40) REVERT: D 100 THR cc_start: 0.9333 (m) cc_final: 0.9117 (p) REVERT: D 163 THR cc_start: 0.7657 (p) cc_final: 0.7412 (t) REVERT: E 8 TYR cc_start: 0.8339 (m-80) cc_final: 0.8069 (m-80) REVERT: E 57 SER cc_start: 0.8152 (m) cc_final: 0.7840 (p) REVERT: F 122 ARG cc_start: 0.8388 (ptm160) cc_final: 0.8187 (ptm160) REVERT: G 98 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7645 (tp30) REVERT: H 39 ASN cc_start: 0.8815 (m110) cc_final: 0.8089 (m110) REVERT: H 51 GLU cc_start: 0.8051 (tp30) cc_final: 0.7794 (tp30) REVERT: I 21 GLN cc_start: 0.8852 (mp10) cc_final: 0.8537 (mp10) REVERT: I 52 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8557 (tmtt) REVERT: I 79 LYS cc_start: 0.7426 (pmmt) cc_final: 0.6644 (ptpp) REVERT: I 144 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8160 (mttm) REVERT: J 73 MET cc_start: 0.7219 (mtt) cc_final: 0.6952 (mtt) REVERT: J 95 GLN cc_start: 0.6325 (mt0) cc_final: 0.5892 (pt0) REVERT: J 212 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8248 (mmmt) REVERT: J 264 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7328 (mm-40) REVERT: K 31 GLN cc_start: 0.8289 (tt0) cc_final: 0.7951 (tp40) REVERT: K 42 GLN cc_start: 0.8865 (tt0) cc_final: 0.8665 (mt0) REVERT: K 134 TYR cc_start: 0.8979 (t80) cc_final: 0.8731 (t80) outliers start: 87 outliers final: 46 residues processed: 624 average time/residue: 0.2019 time to fit residues: 194.1274 Evaluate side-chains 461 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 407 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 10 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 chunk 196 optimal weight: 0.0170 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN B 808 HIS ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN D 5 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 52 ASN F 65 GLN F 106 ASN F 111 GLN H 27 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 ASN J 261 ASN K 130 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.154566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122262 restraints weight = 51431.167| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.31 r_work: 0.3476 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28471 Z= 0.121 Angle : 0.586 9.622 40228 Z= 0.300 Chirality : 0.037 0.221 4852 Planarity : 0.005 0.064 3725 Dihedral : 20.876 174.312 8400 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.06 % Allowed : 18.68 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2372 helix: 0.23 (0.17), residues: 932 sheet: -0.38 (0.24), residues: 451 loop : -1.88 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 454 TYR 0.018 0.002 TYR B 339 PHE 0.025 0.002 PHE B 740 TRP 0.018 0.001 TRP H 9 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00257 (28468) covalent geometry : angle 0.58551 (40228) hydrogen bonds : bond 0.03876 ( 1006) hydrogen bonds : angle 4.35529 ( 2726) metal coordination : bond 0.00235 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 452 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8338 (t0) cc_final: 0.7684 (t0) REVERT: B 201 ASN cc_start: 0.7410 (t0) cc_final: 0.7093 (t0) REVERT: B 225 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7171 (mtmt) REVERT: B 311 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7486 (mmtt) REVERT: B 425 PHE cc_start: 0.8125 (t80) cc_final: 0.7850 (t80) REVERT: B 461 LYS cc_start: 0.8366 (tptp) cc_final: 0.7973 (ttmm) REVERT: B 463 ASN cc_start: 0.6352 (OUTLIER) cc_final: 0.5818 (m-40) REVERT: B 650 SER cc_start: 0.6875 (p) cc_final: 0.6641 (p) REVERT: B 665 GLN cc_start: 0.8392 (pp30) cc_final: 0.7861 (pp30) REVERT: B 803 ASN cc_start: 0.9006 (t160) cc_final: 0.8552 (t0) REVERT: B 819 ASP cc_start: 0.8099 (m-30) cc_final: 0.7890 (m-30) REVERT: C 28 THR cc_start: 0.9099 (m) cc_final: 0.8820 (p) REVERT: C 33 MET cc_start: 0.6374 (mmm) cc_final: 0.6074 (mmt) REVERT: C 47 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7432 (tp) REVERT: C 70 THR cc_start: 0.8475 (p) cc_final: 0.8210 (m) REVERT: C 71 ASP cc_start: 0.8879 (t0) cc_final: 0.8568 (t0) REVERT: C 117 MET cc_start: 0.5913 (mpp) cc_final: 0.5512 (ptp) REVERT: C 175 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8300 (mmm-85) REVERT: D 126 HIS cc_start: 0.7283 (t-90) cc_final: 0.6928 (t-90) REVERT: D 163 THR cc_start: 0.7731 (p) cc_final: 0.7464 (t) REVERT: D 178 TYR cc_start: 0.8475 (m-80) cc_final: 0.8087 (m-80) REVERT: D 216 ILE cc_start: 0.5998 (mm) cc_final: 0.5740 (mt) REVERT: D 277 ILE cc_start: 0.6596 (mm) cc_final: 0.6118 (mm) REVERT: E 57 SER cc_start: 0.8323 (m) cc_final: 0.7983 (p) REVERT: F 65 GLN cc_start: 0.8782 (mm110) cc_final: 0.8097 (mt0) REVERT: F 82 PHE cc_start: 0.8749 (p90) cc_final: 0.8451 (p90) REVERT: F 122 ARG cc_start: 0.8312 (ptm160) cc_final: 0.8100 (ptm160) REVERT: G 41 TYR cc_start: 0.9280 (t80) cc_final: 0.9020 (t80) REVERT: G 98 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7564 (tp30) REVERT: H 15 SER cc_start: 0.8230 (t) cc_final: 0.7875 (p) REVERT: H 39 ASN cc_start: 0.8819 (m110) cc_final: 0.8151 (m110) REVERT: H 49 PHE cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-80) REVERT: H 51 GLU cc_start: 0.7973 (tp30) cc_final: 0.7760 (tp30) REVERT: I 21 GLN cc_start: 0.8693 (mp10) cc_final: 0.8412 (mp10) REVERT: I 186 SER cc_start: 0.8531 (m) cc_final: 0.8108 (t) REVERT: I 208 THR cc_start: 0.8937 (m) cc_final: 0.8681 (p) REVERT: J 73 MET cc_start: 0.7283 (mtt) cc_final: 0.6975 (mtt) REVERT: J 95 GLN cc_start: 0.6238 (mt0) cc_final: 0.5796 (pt0) REVERT: J 222 SER cc_start: 0.7357 (m) cc_final: 0.6756 (p) REVERT: K 31 GLN cc_start: 0.8151 (tt0) cc_final: 0.7905 (tp40) REVERT: K 42 GLN cc_start: 0.8745 (tt0) cc_final: 0.8462 (mt0) outliers start: 67 outliers final: 39 residues processed: 491 average time/residue: 0.1818 time to fit residues: 143.1590 Evaluate side-chains 433 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 392 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 59 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN B 665 GLN B 669 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 106 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN H 27 HIS I 172 GLN J 40 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107462 restraints weight = 50023.155| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.41 r_work: 0.3242 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28471 Z= 0.249 Angle : 0.713 9.843 40228 Z= 0.366 Chirality : 0.042 0.243 4852 Planarity : 0.006 0.072 3725 Dihedral : 20.838 175.509 8400 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.44 % Allowed : 18.50 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2372 helix: 0.41 (0.17), residues: 936 sheet: -0.41 (0.25), residues: 422 loop : -1.72 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 252 TYR 0.026 0.003 TYR B 339 PHE 0.034 0.003 PHE B 657 TRP 0.027 0.002 TRP H 9 HIS 0.015 0.002 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.00549 (28468) covalent geometry : angle 0.71278 (40228) hydrogen bonds : bond 0.05291 ( 1006) hydrogen bonds : angle 4.64834 ( 2726) metal coordination : bond 0.00442 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 415 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8541 (t0) cc_final: 0.8063 (t0) REVERT: B 225 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7648 (mtmt) REVERT: B 311 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7527 (mmtt) REVERT: B 370 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8012 (pp) REVERT: B 416 LEU cc_start: 0.8472 (pp) cc_final: 0.8267 (pp) REVERT: B 632 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.6813 (pmt100) REVERT: B 714 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7570 (tt0) REVERT: B 756 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7732 (t) REVERT: C 29 ASN cc_start: 0.7952 (p0) cc_final: 0.7578 (p0) REVERT: C 33 MET cc_start: 0.6786 (mmm) cc_final: 0.6326 (mmt) REVERT: C 43 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5563 (mp) REVERT: C 70 THR cc_start: 0.8409 (p) cc_final: 0.8152 (m) REVERT: C 131 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (p) REVERT: D 143 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: D 163 THR cc_start: 0.8300 (p) cc_final: 0.8021 (t) REVERT: D 247 SER cc_start: 0.9163 (t) cc_final: 0.8929 (m) REVERT: D 277 ILE cc_start: 0.7820 (mm) cc_final: 0.7383 (mm) REVERT: E 57 SER cc_start: 0.8597 (m) cc_final: 0.8342 (p) REVERT: E 68 CYS cc_start: 0.8568 (m) cc_final: 0.8330 (m) REVERT: F 65 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8262 (mt0) REVERT: F 122 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8170 (ptm160) REVERT: H 15 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8420 (p) REVERT: H 39 ASN cc_start: 0.9019 (m110) cc_final: 0.8267 (m110) REVERT: I 5 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8324 (pp) REVERT: I 21 GLN cc_start: 0.8990 (mp10) cc_final: 0.8776 (mm-40) REVERT: J 110 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (tt) REVERT: J 212 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8280 (ttpp) outliers start: 119 outliers final: 66 residues processed: 497 average time/residue: 0.1864 time to fit residues: 145.8225 Evaluate side-chains 424 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 348 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 133 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 506 ASN B 665 GLN B 803 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN J 95 GLN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 ASN J 264 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110746 restraints weight = 50128.248| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.21 r_work: 0.3306 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28471 Z= 0.120 Angle : 0.580 11.390 40228 Z= 0.296 Chirality : 0.037 0.202 4852 Planarity : 0.004 0.059 3725 Dihedral : 20.750 174.692 8400 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 3.88 % Allowed : 22.02 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2372 helix: 0.80 (0.17), residues: 945 sheet: -0.44 (0.24), residues: 441 loop : -1.63 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 51 TYR 0.016 0.002 TYR D 108 PHE 0.029 0.002 PHE B 740 TRP 0.022 0.001 TRP H 9 HIS 0.005 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00259 (28468) covalent geometry : angle 0.57973 (40228) hydrogen bonds : bond 0.03878 ( 1006) hydrogen bonds : angle 4.35679 ( 2726) metal coordination : bond 0.00288 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 403 time to evaluate : 0.884 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: B 79 ASN cc_start: 0.8454 (t0) cc_final: 0.7973 (t0) REVERT: B 225 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7621 (mtmt) REVERT: B 632 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8438 (ptt90) REVERT: B 650 SER cc_start: 0.7040 (p) cc_final: 0.6714 (p) REVERT: B 756 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7767 (t) REVERT: B 757 PHE cc_start: 0.7827 (t80) cc_final: 0.7522 (t80) REVERT: B 803 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8440 (m-40) REVERT: C 29 ASN cc_start: 0.7879 (p0) cc_final: 0.7536 (p0) REVERT: C 33 MET cc_start: 0.6901 (mmm) cc_final: 0.6372 (mmt) REVERT: C 43 ILE cc_start: 0.6158 (tt) cc_final: 0.5379 (mp) REVERT: C 70 THR cc_start: 0.8593 (p) cc_final: 0.7980 (t) REVERT: D 220 ILE cc_start: 0.9101 (mm) cc_final: 0.8664 (mt) REVERT: D 277 ILE cc_start: 0.7752 (mm) cc_final: 0.7413 (mm) REVERT: E 57 SER cc_start: 0.8512 (m) cc_final: 0.8199 (p) REVERT: F 65 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8450 (mt0) REVERT: F 68 MET cc_start: 0.7512 (ppp) cc_final: 0.5765 (mmp) REVERT: F 82 PHE cc_start: 0.8710 (p90) cc_final: 0.8372 (p90) REVERT: F 122 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8275 (ptm160) REVERT: F 132 ARG cc_start: 0.7577 (mtp85) cc_final: 0.7118 (mtp85) REVERT: G 28 GLN cc_start: 0.9003 (tt0) cc_final: 0.8774 (mt0) REVERT: I 21 GLN cc_start: 0.8924 (mp10) cc_final: 0.8614 (mm-40) REVERT: I 208 THR cc_start: 0.9051 (m) cc_final: 0.8775 (p) REVERT: J 191 ILE cc_start: 0.9158 (pt) cc_final: 0.8615 (mt) REVERT: J 212 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8281 (ttpp) REVERT: J 222 SER cc_start: 0.7684 (m) cc_final: 0.7105 (p) REVERT: K 42 GLN cc_start: 0.8829 (tt0) cc_final: 0.8587 (mt0) outliers start: 85 outliers final: 56 residues processed: 457 average time/residue: 0.1846 time to fit residues: 134.1949 Evaluate side-chains 427 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 368 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 573 ASN B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 197 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107030 restraints weight = 50144.354| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.15 r_work: 0.3251 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28471 Z= 0.168 Angle : 0.609 12.586 40228 Z= 0.308 Chirality : 0.039 0.208 4852 Planarity : 0.004 0.062 3725 Dihedral : 20.684 175.415 8400 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.52 % Allowed : 21.38 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2372 helix: 0.91 (0.17), residues: 948 sheet: -0.44 (0.24), residues: 441 loop : -1.65 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 51 TYR 0.021 0.002 TYR D 143 PHE 0.032 0.002 PHE B 740 TRP 0.036 0.002 TRP H 37 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00369 (28468) covalent geometry : angle 0.60919 (40228) hydrogen bonds : bond 0.04160 ( 1006) hydrogen bonds : angle 4.36616 ( 2726) metal coordination : bond 0.00511 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 379 time to evaluate : 1.023 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: B 79 ASN cc_start: 0.8461 (t0) cc_final: 0.8124 (t0) REVERT: B 225 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7776 (mtmt) REVERT: B 632 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8405 (ptt90) REVERT: B 650 SER cc_start: 0.7294 (p) cc_final: 0.6962 (p) REVERT: B 756 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8128 (t) REVERT: B 757 PHE cc_start: 0.7800 (t80) cc_final: 0.7519 (t80) REVERT: B 774 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8526 (p-80) REVERT: B 793 LEU cc_start: 0.8552 (mm) cc_final: 0.8314 (mp) REVERT: C 29 ASN cc_start: 0.8005 (p0) cc_final: 0.7793 (p0) REVERT: C 33 MET cc_start: 0.7010 (mmm) cc_final: 0.6636 (mmt) REVERT: C 43 ILE cc_start: 0.6231 (tt) cc_final: 0.5571 (mp) REVERT: C 70 THR cc_start: 0.8485 (p) cc_final: 0.7875 (t) REVERT: C 114 MET cc_start: 0.8357 (mmt) cc_final: 0.7921 (ppp) REVERT: C 129 MET cc_start: 0.7292 (ppp) cc_final: 0.6935 (ptt) REVERT: D 194 ILE cc_start: 0.8767 (pt) cc_final: 0.8518 (mt) REVERT: D 220 ILE cc_start: 0.9175 (mm) cc_final: 0.8810 (mt) REVERT: D 277 ILE cc_start: 0.7849 (mm) cc_final: 0.7520 (mm) REVERT: E 8 TYR cc_start: 0.8562 (m-80) cc_final: 0.8347 (m-80) REVERT: E 57 SER cc_start: 0.8625 (m) cc_final: 0.8393 (p) REVERT: F 65 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7794 (mt0) REVERT: F 76 GLN cc_start: 0.5214 (pt0) cc_final: 0.4942 (pm20) REVERT: F 82 PHE cc_start: 0.8745 (p90) cc_final: 0.8369 (p90) REVERT: F 122 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8378 (ptm160) REVERT: F 132 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7265 (mtp85) REVERT: G 28 GLN cc_start: 0.9045 (tt0) cc_final: 0.8783 (mt0) REVERT: G 68 MET cc_start: 0.8974 (ptt) cc_final: 0.8400 (ptt) REVERT: I 21 GLN cc_start: 0.8945 (mp10) cc_final: 0.8660 (mm-40) REVERT: I 208 THR cc_start: 0.9098 (m) cc_final: 0.8767 (p) REVERT: J 36 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (pp) REVERT: J 191 ILE cc_start: 0.9194 (pt) cc_final: 0.8735 (mt) REVERT: J 222 SER cc_start: 0.7739 (m) cc_final: 0.7195 (p) REVERT: K 42 GLN cc_start: 0.8846 (tt0) cc_final: 0.8598 (mt0) outliers start: 99 outliers final: 66 residues processed: 445 average time/residue: 0.1838 time to fit residues: 129.4520 Evaluate side-chains 433 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 363 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 34 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104611 restraints weight = 49747.343| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.18 r_work: 0.3206 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28471 Z= 0.169 Angle : 0.611 12.368 40228 Z= 0.308 Chirality : 0.039 0.198 4852 Planarity : 0.004 0.058 3725 Dihedral : 20.670 176.261 8400 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.75 % Allowed : 21.88 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2372 helix: 0.94 (0.17), residues: 961 sheet: -0.36 (0.25), residues: 422 loop : -1.72 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 51 TYR 0.030 0.002 TYR D 143 PHE 0.033 0.002 PHE B 740 TRP 0.029 0.002 TRP H 37 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00368 (28468) covalent geometry : angle 0.61136 (40228) hydrogen bonds : bond 0.04061 ( 1006) hydrogen bonds : angle 4.38417 ( 2726) metal coordination : bond 0.00456 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 362 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7924 (mtmt) REVERT: B 420 GLU cc_start: 0.7914 (pt0) cc_final: 0.7524 (pt0) REVERT: B 461 LYS cc_start: 0.8493 (tptp) cc_final: 0.8108 (ttmm) REVERT: B 462 LEU cc_start: 0.6960 (tp) cc_final: 0.6722 (tt) REVERT: B 632 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8334 (ptt90) REVERT: C 29 ASN cc_start: 0.7877 (p0) cc_final: 0.7663 (p0) REVERT: C 33 MET cc_start: 0.6505 (mmm) cc_final: 0.6255 (mmt) REVERT: C 43 ILE cc_start: 0.5905 (tt) cc_final: 0.5288 (mp) REVERT: C 70 THR cc_start: 0.8658 (p) cc_final: 0.8085 (t) REVERT: C 113 TYR cc_start: 0.7441 (t80) cc_final: 0.7231 (t80) REVERT: C 114 MET cc_start: 0.8235 (mmt) cc_final: 0.7888 (ppp) REVERT: C 129 MET cc_start: 0.7612 (ppp) cc_final: 0.7139 (ptt) REVERT: D 220 ILE cc_start: 0.9213 (mm) cc_final: 0.8864 (mt) REVERT: E 57 SER cc_start: 0.8646 (m) cc_final: 0.8367 (p) REVERT: F 65 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8192 (mt0) REVERT: F 68 MET cc_start: 0.5520 (ppp) cc_final: 0.4658 (mtp) REVERT: F 82 PHE cc_start: 0.8720 (p90) cc_final: 0.8353 (p90) REVERT: F 84 TYR cc_start: 0.8907 (p90) cc_final: 0.8617 (p90) REVERT: F 122 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8387 (ptm160) REVERT: F 125 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7780 (mtp180) REVERT: G 28 GLN cc_start: 0.9046 (tt0) cc_final: 0.8844 (mt0) REVERT: G 68 MET cc_start: 0.8963 (ptt) cc_final: 0.8746 (ptt) REVERT: H 44 ARG cc_start: 0.8071 (tpp-160) cc_final: 0.7636 (mmm160) REVERT: I 208 THR cc_start: 0.9134 (m) cc_final: 0.8759 (p) REVERT: J 36 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8017 (pp) REVERT: J 63 ILE cc_start: 0.8747 (mm) cc_final: 0.8480 (mt) REVERT: J 222 SER cc_start: 0.7871 (m) cc_final: 0.7311 (p) outliers start: 104 outliers final: 80 residues processed: 433 average time/residue: 0.1888 time to fit residues: 131.6446 Evaluate side-chains 420 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 337 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 190 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 502 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN C 38 HIS C 160 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS H 70 ASN I 151 ASN ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098717 restraints weight = 49633.778| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.8557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28471 Z= 0.279 Angle : 0.738 11.969 40228 Z= 0.375 Chirality : 0.044 0.285 4852 Planarity : 0.005 0.077 3725 Dihedral : 20.774 179.808 8400 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 4.93 % Allowed : 22.06 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2372 helix: 0.60 (0.17), residues: 963 sheet: -0.47 (0.25), residues: 407 loop : -1.87 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 202 TYR 0.029 0.003 TYR K 134 PHE 0.034 0.003 PHE D 253 TRP 0.030 0.002 TRP H 9 HIS 0.009 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00621 (28468) covalent geometry : angle 0.73807 (40228) hydrogen bonds : bond 0.05244 ( 1006) hydrogen bonds : angle 4.72269 ( 2726) metal coordination : bond 0.00735 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 360 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8384 (pp30) REVERT: B 507 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8441 (tp-100) REVERT: B 632 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8441 (ptt90) REVERT: C 29 ASN cc_start: 0.7657 (p0) cc_final: 0.7170 (p0) REVERT: C 70 THR cc_start: 0.8742 (p) cc_final: 0.8186 (t) REVERT: C 71 ASP cc_start: 0.9032 (t0) cc_final: 0.8736 (t0) REVERT: C 114 MET cc_start: 0.8200 (mmt) cc_final: 0.7829 (ppp) REVERT: C 129 MET cc_start: 0.7662 (ppp) cc_final: 0.7369 (ptt) REVERT: E 8 TYR cc_start: 0.8697 (m-80) cc_final: 0.8464 (m-80) REVERT: E 103 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8262 (ttp) REVERT: F 65 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8172 (mt0) REVERT: F 68 MET cc_start: 0.5383 (ppp) cc_final: 0.4689 (mtp) REVERT: F 84 TYR cc_start: 0.9128 (p90) cc_final: 0.8840 (p90) REVERT: F 125 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7650 (mtp180) REVERT: F 132 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7647 (mtp85) REVERT: G 28 GLN cc_start: 0.9141 (tt0) cc_final: 0.8880 (mt0) REVERT: G 68 MET cc_start: 0.8987 (ptt) cc_final: 0.8654 (ptt) REVERT: J 63 ILE cc_start: 0.8980 (mm) cc_final: 0.8686 (mt) REVERT: J 110 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8763 (tt) REVERT: J 209 SER cc_start: 0.9251 (p) cc_final: 0.8965 (m) REVERT: J 222 SER cc_start: 0.8313 (m) cc_final: 0.7988 (p) outliers start: 108 outliers final: 79 residues processed: 431 average time/residue: 0.1915 time to fit residues: 130.6134 Evaluate side-chains 414 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 252 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 250 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN C 83 HIS C 165 GLN D 278 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102039 restraints weight = 49491.573| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.23 r_work: 0.3154 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28471 Z= 0.172 Angle : 0.654 11.433 40228 Z= 0.331 Chirality : 0.040 0.273 4852 Planarity : 0.005 0.060 3725 Dihedral : 20.719 179.014 8400 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.11 % Allowed : 23.71 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2372 helix: 0.84 (0.17), residues: 957 sheet: -0.51 (0.25), residues: 417 loop : -1.82 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 67 TYR 0.029 0.002 TYR K 134 PHE 0.030 0.002 PHE B 740 TRP 0.025 0.002 TRP H 9 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00383 (28468) covalent geometry : angle 0.65435 (40228) hydrogen bonds : bond 0.04249 ( 1006) hydrogen bonds : angle 4.55461 ( 2726) metal coordination : bond 0.00533 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8752 (t0) cc_final: 0.8308 (m-40) REVERT: B 384 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8287 (pp30) REVERT: B 632 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8378 (ptt90) REVERT: B 665 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (pp30) REVERT: C 43 ILE cc_start: 0.6301 (tt) cc_final: 0.5630 (mp) REVERT: C 70 THR cc_start: 0.8767 (p) cc_final: 0.8218 (t) REVERT: C 71 ASP cc_start: 0.8994 (t0) cc_final: 0.8720 (t0) REVERT: C 78 TYR cc_start: 0.8263 (t80) cc_final: 0.7847 (t80) REVERT: C 113 TYR cc_start: 0.7529 (t80) cc_final: 0.7323 (t80) REVERT: C 114 MET cc_start: 0.8186 (mmt) cc_final: 0.7797 (ppp) REVERT: C 129 MET cc_start: 0.7570 (ppp) cc_final: 0.7284 (ptt) REVERT: C 150 ASP cc_start: 0.5503 (t0) cc_final: 0.5159 (m-30) REVERT: D 247 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (m) REVERT: E 8 TYR cc_start: 0.8606 (m-80) cc_final: 0.8331 (m-80) REVERT: E 46 LYS cc_start: 0.9275 (pptt) cc_final: 0.9007 (pttp) REVERT: F 65 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8142 (mt0) REVERT: F 68 MET cc_start: 0.5269 (ppp) cc_final: 0.4676 (mtp) REVERT: F 84 TYR cc_start: 0.9006 (p90) cc_final: 0.8735 (p90) REVERT: F 125 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7688 (mtp180) REVERT: F 132 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7538 (mtp85) REVERT: G 28 GLN cc_start: 0.9124 (tt0) cc_final: 0.8851 (mt0) REVERT: H 44 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.7840 (mmp-170) REVERT: I 208 THR cc_start: 0.9166 (m) cc_final: 0.8870 (p) REVERT: J 63 ILE cc_start: 0.8972 (mm) cc_final: 0.8698 (mt) REVERT: J 222 SER cc_start: 0.8203 (m) cc_final: 0.7925 (p) REVERT: K 99 THR cc_start: 0.9032 (m) cc_final: 0.8731 (p) outliers start: 90 outliers final: 69 residues processed: 421 average time/residue: 0.1884 time to fit residues: 126.6518 Evaluate side-chains 411 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 339 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 73 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 735 ASN B 803 ASN D 278 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 GLN K 17 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103946 restraints weight = 49820.371| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.17 r_work: 0.3199 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.8630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28471 Z= 0.132 Angle : 0.624 11.525 40228 Z= 0.315 Chirality : 0.038 0.271 4852 Planarity : 0.004 0.057 3725 Dihedral : 20.641 177.042 8400 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.20 % Allowed : 24.53 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2372 helix: 0.97 (0.17), residues: 955 sheet: -0.44 (0.25), residues: 417 loop : -1.78 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 67 TYR 0.030 0.002 TYR K 134 PHE 0.030 0.002 PHE B 740 TRP 0.025 0.002 TRP H 37 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00292 (28468) covalent geometry : angle 0.62378 (40228) hydrogen bonds : bond 0.03914 ( 1006) hydrogen bonds : angle 4.45533 ( 2726) metal coordination : bond 0.00431 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 365 time to evaluate : 0.982 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: B 79 ASN cc_start: 0.8734 (t0) cc_final: 0.8309 (m-40) REVERT: B 466 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.6140 (pp30) REVERT: B 632 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8346 (ptt90) REVERT: B 768 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (t) REVERT: B 774 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8685 (p-80) REVERT: C 43 ILE cc_start: 0.6188 (tt) cc_final: 0.5530 (mp) REVERT: C 69 TYR cc_start: 0.5710 (m-10) cc_final: 0.5499 (m-80) REVERT: C 70 THR cc_start: 0.8783 (p) cc_final: 0.8237 (t) REVERT: C 71 ASP cc_start: 0.8968 (t0) cc_final: 0.8690 (t0) REVERT: C 78 TYR cc_start: 0.8084 (t80) cc_final: 0.7733 (t80) REVERT: C 113 TYR cc_start: 0.7402 (t80) cc_final: 0.7184 (t80) REVERT: C 114 MET cc_start: 0.8281 (mmt) cc_final: 0.7775 (ppp) REVERT: C 129 MET cc_start: 0.7444 (ppp) cc_final: 0.7177 (ptt) REVERT: C 150 ASP cc_start: 0.5573 (t0) cc_final: 0.5104 (m-30) REVERT: E 8 TYR cc_start: 0.8558 (m-80) cc_final: 0.8289 (m-80) REVERT: E 46 LYS cc_start: 0.9188 (pptt) cc_final: 0.8886 (pttp) REVERT: F 68 MET cc_start: 0.5468 (ppp) cc_final: 0.4796 (mtp) REVERT: F 82 PHE cc_start: 0.8604 (p90) cc_final: 0.8257 (p90) REVERT: G 28 GLN cc_start: 0.9071 (tt0) cc_final: 0.8818 (mt0) REVERT: G 33 ILE cc_start: 0.9243 (mm) cc_final: 0.8935 (tt) REVERT: H 44 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7954 (mmp-170) REVERT: I 208 THR cc_start: 0.9152 (m) cc_final: 0.8882 (p) REVERT: J 63 ILE cc_start: 0.8877 (mm) cc_final: 0.8612 (mt) REVERT: J 222 SER cc_start: 0.8142 (m) cc_final: 0.7839 (p) REVERT: K 31 GLN cc_start: 0.8941 (tp40) cc_final: 0.8511 (tp40) REVERT: K 99 THR cc_start: 0.8984 (m) cc_final: 0.8704 (p) outliers start: 70 outliers final: 57 residues processed: 408 average time/residue: 0.1924 time to fit residues: 124.8858 Evaluate side-chains 400 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 208 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 135 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 HIS ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104585 restraints weight = 49454.184| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.14 r_work: 0.3209 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28471 Z= 0.125 Angle : 0.622 11.773 40228 Z= 0.314 Chirality : 0.038 0.280 4852 Planarity : 0.005 0.069 3725 Dihedral : 20.607 175.799 8400 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.02 % Allowed : 25.08 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2372 helix: 1.04 (0.17), residues: 955 sheet: -0.39 (0.25), residues: 425 loop : -1.73 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 549 TYR 0.029 0.002 TYR K 134 PHE 0.032 0.002 PHE B 740 TRP 0.027 0.001 TRP H 37 HIS 0.009 0.001 HIS G 56 Details of bonding type rmsd covalent geometry : bond 0.00279 (28468) covalent geometry : angle 0.62164 (40228) hydrogen bonds : bond 0.03825 ( 1006) hydrogen bonds : angle 4.42263 ( 2726) metal coordination : bond 0.00463 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6827.25 seconds wall clock time: 117 minutes 56.72 seconds (7076.72 seconds total)