Starting phenix.real_space_refine on Mon Sep 14 00:41:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_9616_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_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 { model { file = "/net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_9616_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_9616_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_9616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6agb_9616/09_2026/6agb_9616.map" } 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-2.2.1-6174/lib/python3.11/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: 5.41, per 1000 atoms: 0.20 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: 2.30 Conformation dependent library (CDL) restraints added in 869.9 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: 3.61 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: 5.89 Time building geometry restraints manager: 3.10 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=" N9 A A 204 " pdb=" C4 A A 204 " ideal model delta sigma weight residual 1.374 1.394 -0.020 6.00e-03 2.78e+04 1.14e+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 ... (remaining 28463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 39116 2.52 - 5.05: 992 5.05 - 7.57: 100 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=" N1 C A 135 " pdb=" C2 C A 135 " pdb=" O2 C A 135 " ideal model delta sigma weight residual 118.90 123.24 -4.34 6.00e-01 2.78e+00 5.24e+01 angle pdb=" N1 C A 182 " pdb=" C2 C A 182 " pdb=" O2 C A 182 " ideal model delta sigma weight residual 118.90 123.16 -4.26 6.00e-01 2.78e+00 5.03e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 119.70 127.25 -7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" C3' A A 367 " pdb=" O3' A A 367 " pdb=" P G A 368 " ideal model delta sigma weight residual 119.70 126.90 -7.20 1.20e+00 6.94e-01 3.60e+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: 4071 0.076 - 0.152: 733 0.152 - 0.227: 44 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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= 0.301 Angle : 0.917 12.614 40228 Z= 0.663 Chirality : 0.056 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/Z covalent geometry : bond 0.00337 / 0.23 (28468) covalent geometry : angle 0.91747 / 0.66 (40228) hydrogen bonds : bond 0.16521 / 16.42 ( 1006) hydrogen bonds : angle 6.94372 / 8.87 ( 2726) metal coordination : bond 0.57345 / 42.01 ( 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 : 1.064 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: 0.7333 (t0) REVERT: B 146 GLN cc_start: 0.8079 (pt0) cc_final: 0.7691 (pt0) REVERT: B 217 VAL cc_start: 0.7608 (t) cc_final: 0.7305 (m) REVERT: B 311 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6900 (mmtt) REVERT: B 342 ASN cc_start: 0.7845 (t0) cc_final: 0.7633 (t0) REVERT: B 452 ASP cc_start: 0.7214 (t0) cc_final: 0.5154 (t70) REVERT: B 588 GLN cc_start: 0.8278 (tt0) cc_final: 0.7955 (tt0) REVERT: C 19 TYR cc_start: 0.8022 (m-80) cc_final: 0.7686 (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: 0.6371 (t70) REVERT: C 103 VAL cc_start: 0.7941 (t) cc_final: 0.7671 (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: 0.7015 (p) REVERT: G 41 TYR cc_start: 0.8703 (t80) cc_final: 0.8370 (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: 0.7081 (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: 0.7646 (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: 0.7133 (tm-30) REVERT: I 159 VAL cc_start: 0.9195 (t) cc_final: 0.8869 (t) REVERT: J 191 ILE cc_start: 0.9206 (pt) cc_final: 0.8987 (pt) REVERT: K 134 TYR cc_start: 0.8083 (t80) cc_final: 0.7762 (t80) outliers start: 4 outliers final: 0 residues processed: 929 average time/residue: 0.2128 time to fit residues: 295.2576 Evaluate side-chains 493 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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: 30.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 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: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 90 GLN B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 463 ASN B 479 HIS B 488 ASN B 505 ASN B 507 GLN B 590 GLN B 642 HIS B 665 GLN B 669 ASN B 675 GLN B 677 ASN B 704 ASN B 803 ASN B 808 HIS C 25 ASN C 40 GLN C 48 GLN C 73 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 95 ASN D 197 GLN E 50 GLN E 139 ASN F 8 ASN F 37 ASN F 54 ASN F 76 GLN F 87 HIS G 28 GLN G 58 GLN H 40 ASN H 59 HIS 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 Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.166039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135473 restraints weight = 52864.912| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.40 r_work: 0.3696 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28471 Z= 0.222 Angle : 0.713 9.889 40228 Z= 0.376 Chirality : 0.044 0.577 4852 Planarity : 0.006 0.084 3725 Dihedral : 21.090 179.319 8400 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 3.75 % Allowed : 14.48 % Favored : 81.77 % 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: -2.17 (0.16), residues: 2372 helix: -0.96 (0.15), residues: 929 sheet: -0.52 (0.24), residues: 436 loop : -2.26 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 115 TYR 0.025 0.002 TYR B 602 PHE 0.028 0.003 PHE I 45 TRP 0.021 0.002 TRP H 9 HIS 0.011 0.002 HIS B 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (28468) covalent geometry : angle 0.71280 / 0.38 (40228) hydrogen bonds : bond 0.05566 / 5.92 ( 1006) hydrogen bonds : angle 4.90089 / 6.51 ( 2726) metal coordination : bond 0.03344 / 1.80 ( 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 597 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 515 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8171 (t0) cc_final: 0.7548 (t0) REVERT: B 146 GLN cc_start: 0.8363 (pt0) cc_final: 0.7991 (pt0) REVERT: B 166 MET cc_start: 0.8238 (ptm) cc_final: 0.7937 (ptm) REVERT: B 201 ASN cc_start: 0.6870 (t0) cc_final: 0.6601 (t0) REVERT: B 282 SER cc_start: 0.8595 (m) cc_final: 0.8378 (p) REVERT: B 288 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8756 (ttm) REVERT: B 311 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7177 (mmtt) REVERT: B 370 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5753 (pp) REVERT: B 461 LYS cc_start: 0.8149 (tptp) cc_final: 0.7265 (ttmm) REVERT: B 463 ASN cc_start: 0.6097 (OUTLIER) cc_final: 0.5665 (m-40) REVERT: B 588 GLN cc_start: 0.8885 (tt0) cc_final: 0.8553 (tt0) REVERT: B 632 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7693 (ptt90) REVERT: B 650 SER cc_start: 0.6539 (p) cc_final: 0.6315 (p) REVERT: B 665 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7899 (pp30) REVERT: B 756 THR cc_start: 0.6021 (OUTLIER) cc_final: 0.5679 (t) REVERT: B 771 GLU cc_start: 0.7975 (tt0) cc_final: 0.7730 (tt0) REVERT: B 803 ASN cc_start: 0.8805 (t160) cc_final: 0.8575 (t0) REVERT: C 19 TYR cc_start: 0.8465 (m-80) cc_final: 0.8111 (m-10) REVERT: C 28 THR cc_start: 0.9179 (m) cc_final: 0.8940 (p) REVERT: C 47 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7213 (tp) REVERT: C 129 MET cc_start: 0.7185 (ptm) cc_final: 0.5475 (mtm) REVERT: C 147 ASP cc_start: 0.7045 (p0) cc_final: 0.6728 (p0) REVERT: D 233 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8492 (mt-10) REVERT: E 57 SER cc_start: 0.7966 (m) cc_final: 0.7569 (p) REVERT: E 67 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7986 (mtmt) REVERT: F 82 PHE cc_start: 0.8395 (p90) cc_final: 0.8119 (p90) REVERT: F 122 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7213 (ptm160) REVERT: G 98 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7357 (tp30) REVERT: H 39 ASN cc_start: 0.8581 (m110) cc_final: 0.8111 (m-40) REVERT: H 57 PHE cc_start: 0.8625 (m-80) cc_final: 0.8387 (m-80) REVERT: I 5 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7784 (pp) REVERT: I 21 GLN cc_start: 0.8670 (mp10) cc_final: 0.8402 (mp10) REVERT: I 79 LYS cc_start: 0.6502 (pmmt) cc_final: 0.5674 (ptpp) REVERT: I 157 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7676 (tm-30) REVERT: I 238 LEU cc_start: 0.7389 (mt) cc_final: 0.6563 (pp) REVERT: J 73 MET cc_start: 0.7024 (mtt) cc_final: 0.6780 (mtt) REVERT: J 95 GLN cc_start: 0.6224 (mt0) cc_final: 0.5771 (pt0) REVERT: K 134 TYR cc_start: 0.8620 (t80) cc_final: 0.8308 (t80) outliers start: 82 outliers final: 44 residues processed: 569 average time/residue: 0.1821 time to fit residues: 164.2828 Evaluate side-chains 467 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 414 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 463 ASN 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 817 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 105 LYS 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 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 E residue 139 ASN Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 60 SER 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 80 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 11 GLN 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 143 HIS Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain K residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 10 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 115 optimal weight: 0.0970 chunk 122 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 259 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 704 ASN C 106 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 139 ASN G 58 GLN H 27 HIS I 143 HIS K 35 HIS ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134192 restraints weight = 52744.946| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.46 r_work: 0.3658 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28471 Z= 0.126 Angle : 0.588 9.397 40228 Z= 0.311 Chirality : 0.040 0.537 4852 Planarity : 0.005 0.071 3725 Dihedral : 20.924 179.226 8400 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 3.38 % Allowed : 17.27 % Favored : 79.35 % 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: -1.47 (0.17), residues: 2372 helix: -0.19 (0.16), residues: 940 sheet: -0.42 (0.24), residues: 447 loop : -1.98 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 780 TYR 0.017 0.002 TYR J 160 PHE 0.031 0.002 PHE D 207 TRP 0.018 0.001 TRP H 9 HIS 0.007 0.001 HIS I 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (28468) covalent geometry : angle 0.58755 / 0.31 (40228) hydrogen bonds : bond 0.04605 / 4.99 ( 1006) hydrogen bonds : angle 4.53539 / 6.03 ( 2726) metal coordination : bond 0.00626 / 0.36 ( 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 537 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 463 time to evaluate : 0.778 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: B 79 ASN cc_start: 0.8162 (t0) cc_final: 0.7516 (t0) REVERT: B 146 GLN cc_start: 0.8372 (pt0) cc_final: 0.8021 (pt0) REVERT: B 201 ASN cc_start: 0.6951 (t0) cc_final: 0.6603 (t0) REVERT: B 225 LYS cc_start: 0.7111 (mttt) cc_final: 0.6724 (mtmt) REVERT: B 282 SER cc_start: 0.8507 (m) cc_final: 0.8195 (p) REVERT: B 311 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7164 (mmtt) REVERT: B 588 GLN cc_start: 0.8936 (tt0) cc_final: 0.8585 (tt0) REVERT: B 650 SER cc_start: 0.6560 (p) cc_final: 0.6351 (p) REVERT: B 665 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7685 (pp30) REVERT: B 756 THR cc_start: 0.6123 (OUTLIER) cc_final: 0.5812 (t) REVERT: B 805 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8552 (mtt-85) REVERT: B 819 ASP cc_start: 0.7432 (m-30) cc_final: 0.7184 (m-30) REVERT: C 28 THR cc_start: 0.9231 (m) cc_final: 0.8925 (p) REVERT: C 29 ASN cc_start: 0.7900 (p0) cc_final: 0.7200 (p0) REVERT: C 117 MET cc_start: 0.5896 (mpp) cc_final: 0.5512 (ptp) REVERT: C 123 GLN cc_start: 0.6719 (tm-30) cc_final: 0.6361 (tm-30) REVERT: C 129 MET cc_start: 0.7151 (ptm) cc_final: 0.6490 (tmm) REVERT: D 100 THR cc_start: 0.9167 (m) cc_final: 0.8894 (p) REVERT: D 163 THR cc_start: 0.7182 (p) cc_final: 0.6961 (t) REVERT: E 57 SER cc_start: 0.8160 (m) cc_final: 0.7736 (p) REVERT: F 82 PHE cc_start: 0.8452 (p90) cc_final: 0.8184 (p90) REVERT: G 98 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7384 (tp30) REVERT: G 125 GLN cc_start: 0.7865 (tp40) cc_final: 0.7441 (mt0) REVERT: H 51 GLU cc_start: 0.7910 (tp30) cc_final: 0.7653 (tp30) REVERT: H 57 PHE cc_start: 0.8559 (m-80) cc_final: 0.8334 (m-80) REVERT: H 123 MET cc_start: 0.6185 (mmt) cc_final: 0.5858 (mmp) REVERT: I 21 GLN cc_start: 0.8723 (mp10) cc_final: 0.8493 (mp10) REVERT: I 73 MET cc_start: 0.7886 (tpp) cc_final: 0.7549 (tpp) REVERT: I 79 LYS cc_start: 0.6828 (pmmt) cc_final: 0.6396 (ptpp) REVERT: I 157 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7790 (tm-30) REVERT: I 204 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8640 (tt) REVERT: I 208 THR cc_start: 0.8993 (m) cc_final: 0.8601 (p) REVERT: I 238 LEU cc_start: 0.7496 (mt) cc_final: 0.6844 (pp) REVERT: J 95 GLN cc_start: 0.6195 (mt0) cc_final: 0.5778 (pt0) REVERT: J 222 SER cc_start: 0.7235 (m) cc_final: 0.6609 (p) outliers start: 74 outliers final: 40 residues processed: 505 average time/residue: 0.1781 time to fit residues: 144.8032 Evaluate side-chains 439 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 396 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 728 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 794 GLN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR 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 54 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 59 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 247 optimal weight: 0.0570 chunk 45 optimal weight: 9.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 704 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS H 27 HIS I 143 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.154800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122716 restraints weight = 51488.598| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.28 r_work: 0.3490 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28471 Z= 0.185 Angle : 0.627 11.410 40228 Z= 0.330 Chirality : 0.041 0.429 4852 Planarity : 0.005 0.092 3725 Dihedral : 20.820 178.588 8400 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.63 % Rotamer: Outliers : 4.29 % Allowed : 17.41 % Favored : 78.30 % 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: -1.15 (0.17), residues: 2372 helix: 0.24 (0.17), residues: 942 sheet: -0.50 (0.24), residues: 445 loop : -1.85 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 165 TYR 0.026 0.002 TYR B 602 PHE 0.029 0.002 PHE B 657 TRP 0.021 0.002 TRP H 9 HIS 0.007 0.002 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (28468) covalent geometry : angle 0.62748 / 0.33 (40228) hydrogen bonds : bond 0.04840 / 5.20 ( 1006) hydrogen bonds : angle 4.46396 / 5.93 ( 2726) metal coordination : bond 0.00151 / 0.15 ( 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 540 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 446 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8263 (t0) cc_final: 0.7579 (t0) REVERT: B 146 GLN cc_start: 0.8630 (pt0) cc_final: 0.8352 (pt0) REVERT: B 201 ASN cc_start: 0.7395 (t0) cc_final: 0.7086 (t0) REVERT: B 225 LYS cc_start: 0.7629 (mttt) cc_final: 0.7121 (mtmt) REVERT: B 311 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7468 (mmtt) REVERT: B 461 LYS cc_start: 0.8330 (tptp) cc_final: 0.7544 (ttmm) REVERT: B 530 LYS cc_start: 0.8022 (pttm) cc_final: 0.7197 (mmtt) REVERT: B 543 ILE cc_start: 0.9074 (pt) cc_final: 0.8802 (pt) REVERT: B 588 GLN cc_start: 0.8982 (tt0) cc_final: 0.8683 (tt0) REVERT: B 632 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8025 (ptt90) REVERT: B 650 SER cc_start: 0.7170 (p) cc_final: 0.6937 (p) REVERT: B 655 ASP cc_start: 0.8092 (t70) cc_final: 0.7680 (t0) REVERT: B 819 ASP cc_start: 0.7988 (m-30) cc_final: 0.7711 (m-30) REVERT: C 72 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7970 (t80) REVERT: C 104 LEU cc_start: 0.8978 (pp) cc_final: 0.8403 (tp) REVERT: C 117 MET cc_start: 0.5881 (mpp) cc_final: 0.5561 (ptp) REVERT: C 129 MET cc_start: 0.7026 (ptm) cc_final: 0.6457 (tmm) REVERT: D 100 THR cc_start: 0.9276 (m) cc_final: 0.8952 (p) REVERT: D 126 HIS cc_start: 0.6862 (t-90) cc_final: 0.6635 (t70) REVERT: D 163 THR cc_start: 0.7781 (p) cc_final: 0.7562 (t) REVERT: D 178 TYR cc_start: 0.8512 (m-80) cc_final: 0.8260 (m-80) REVERT: E 57 SER cc_start: 0.8196 (m) cc_final: 0.7830 (p) REVERT: F 65 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8285 (mt0) REVERT: F 68 MET cc_start: 0.7424 (ppp) cc_final: 0.5022 (mmp) REVERT: F 133 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6951 (mp) REVERT: G 98 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7503 (tp30) REVERT: G 125 GLN cc_start: 0.7928 (tp40) cc_final: 0.7476 (mt0) REVERT: H 36 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8103 (tp40) REVERT: H 91 VAL cc_start: 0.7315 (t) cc_final: 0.7042 (t) REVERT: H 123 MET cc_start: 0.6034 (mmt) cc_final: 0.5805 (mmt) REVERT: I 21 GLN cc_start: 0.8696 (mp10) cc_final: 0.8448 (mp10) REVERT: I 73 MET cc_start: 0.8044 (tpp) cc_final: 0.7694 (mmm) REVERT: I 78 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7335 (pt) REVERT: I 238 LEU cc_start: 0.7444 (mt) cc_final: 0.6673 (pp) REVERT: J 95 GLN cc_start: 0.6305 (mt0) cc_final: 0.5934 (pt0) REVERT: J 115 LYS cc_start: 0.6652 (pttm) cc_final: 0.6237 (pttt) REVERT: K 31 GLN cc_start: 0.8146 (tt0) cc_final: 0.7861 (tp40) REVERT: K 125 ILE cc_start: 0.8521 (tp) cc_final: 0.8316 (tt) REVERT: K 134 TYR cc_start: 0.8900 (t80) cc_final: 0.8292 (t80) outliers start: 94 outliers final: 64 residues processed: 503 average time/residue: 0.1784 time to fit residues: 145.7129 Evaluate side-chains 454 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 386 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU 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 728 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 97 ASP 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 113 THR Chi-restraints excluded: chain D residue 138 ASP 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 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS 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 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 177 VAL 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 100 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 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: 5.9990 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 231 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 160 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 803 ASN C 123 GLN C 165 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN H 27 HIS H 70 ASN I 143 HIS J 213 ASN J 261 ASN J 264 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123592 restraints weight = 51411.050| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.28 r_work: 0.3505 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28471 Z= 0.111 Angle : 0.564 11.866 40228 Z= 0.294 Chirality : 0.038 0.375 4852 Planarity : 0.004 0.066 3725 Dihedral : 20.815 178.394 8400 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.56 % Allowed : 20.15 % Favored : 76.29 % 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: -0.77 (0.17), residues: 2372 helix: 0.65 (0.17), residues: 945 sheet: -0.39 (0.24), residues: 440 loop : -1.71 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 51 TYR 0.018 0.002 TYR K 134 PHE 0.032 0.002 PHE B 740 TRP 0.020 0.001 TRP H 9 HIS 0.010 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (28468) covalent geometry : angle 0.56398 / 0.29 (40228) hydrogen bonds : bond 0.04041 / 4.33 ( 1006) hydrogen bonds : angle 4.32047 / 5.77 ( 2726) metal coordination : bond 0.00312 / 0.20 ( 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 485 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 407 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8273 (t0) cc_final: 0.7581 (t0) REVERT: B 146 GLN cc_start: 0.8550 (pt0) cc_final: 0.8332 (pt0) REVERT: B 201 ASN cc_start: 0.7383 (t0) cc_final: 0.7025 (t0) REVERT: B 225 LYS cc_start: 0.7664 (mttt) cc_final: 0.7156 (mtmt) REVERT: B 311 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7474 (mmtt) REVERT: B 461 LYS cc_start: 0.8231 (tptp) cc_final: 0.7488 (ttmm) REVERT: B 530 LYS cc_start: 0.7992 (pttm) cc_final: 0.7170 (mmtt) REVERT: B 588 GLN cc_start: 0.8955 (tt0) cc_final: 0.8682 (tt0) REVERT: B 632 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7980 (ptt90) REVERT: B 650 SER cc_start: 0.6411 (p) cc_final: 0.6171 (p) REVERT: B 655 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 756 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6838 (t) REVERT: B 819 ASP cc_start: 0.7931 (m-30) cc_final: 0.7644 (m-30) REVERT: C 117 MET cc_start: 0.5745 (mpp) cc_final: 0.5460 (ptp) REVERT: D 100 THR cc_start: 0.9253 (m) cc_final: 0.8934 (p) REVERT: D 163 THR cc_start: 0.7789 (p) cc_final: 0.7573 (t) REVERT: D 178 TYR cc_start: 0.8414 (m-80) cc_final: 0.8144 (m-80) REVERT: D 277 ILE cc_start: 0.6556 (mm) cc_final: 0.6104 (mm) REVERT: E 57 SER cc_start: 0.8263 (m) cc_final: 0.7971 (p) REVERT: F 10 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (mm) REVERT: F 65 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8320 (mt0) REVERT: F 68 MET cc_start: 0.7502 (ppp) cc_final: 0.5048 (mmp) REVERT: F 82 PHE cc_start: 0.8630 (p90) cc_final: 0.8268 (p90) REVERT: F 126 ASN cc_start: 0.8413 (t0) cc_final: 0.8047 (t0) REVERT: F 132 ARG cc_start: 0.6605 (mtp85) cc_final: 0.6278 (mtp85) REVERT: F 133 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6951 (mp) REVERT: G 98 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7532 (tp30) REVERT: G 125 GLN cc_start: 0.7988 (tp40) cc_final: 0.7535 (mt0) REVERT: H 36 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8210 (tp40) REVERT: I 73 MET cc_start: 0.8224 (tpp) cc_final: 0.7652 (mmt) REVERT: I 78 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.6824 (pt) REVERT: I 208 THR cc_start: 0.9000 (m) cc_final: 0.8689 (p) REVERT: I 238 LEU cc_start: 0.7717 (mt) cc_final: 0.6947 (pp) REVERT: J 95 GLN cc_start: 0.6238 (mt0) cc_final: 0.5896 (pt0) REVERT: J 115 LYS cc_start: 0.6547 (pttm) cc_final: 0.6163 (pttt) REVERT: J 213 ASN cc_start: 0.7196 (t0) cc_final: 0.6934 (t0) REVERT: K 31 GLN cc_start: 0.8107 (tt0) cc_final: 0.7814 (tp40) REVERT: K 134 TYR cc_start: 0.8978 (t80) cc_final: 0.8365 (t80) outliers start: 78 outliers final: 44 residues processed: 455 average time/residue: 0.1727 time to fit residues: 127.3096 Evaluate side-chains 437 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 387 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS 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 H residue 119 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 41 optimal weight: 0.0370 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 221 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 704 ASN B 803 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS G 56 HIS H 27 HIS H 70 ASN I 143 HIS K 35 HIS K 42 GLN K 130 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123493 restraints weight = 51292.786| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.29 r_work: 0.3501 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 28471 Z= 0.105 Angle : 0.548 11.702 40228 Z= 0.284 Chirality : 0.038 0.373 4852 Planarity : 0.004 0.063 3725 Dihedral : 20.757 178.248 8400 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.56 % Allowed : 20.47 % Favored : 75.97 % 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: -0.58 (0.17), residues: 2372 helix: 0.91 (0.17), residues: 944 sheet: -0.32 (0.25), residues: 436 loop : -1.69 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 51 TYR 0.020 0.001 TYR D 130 PHE 0.033 0.002 PHE B 740 TRP 0.018 0.001 TRP H 9 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (28468) covalent geometry : angle 0.54774 / 0.28 (40228) hydrogen bonds : bond 0.03814 / 4.08 ( 1006) hydrogen bonds : angle 4.25243 / 5.73 ( 2726) metal coordination : bond 0.00054 / 0.05 ( 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 482 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 404 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8289 (t0) cc_final: 0.7631 (t0) REVERT: B 146 GLN cc_start: 0.8574 (pt0) cc_final: 0.8345 (pt0) REVERT: B 201 ASN cc_start: 0.7495 (t0) cc_final: 0.7159 (t0) REVERT: B 225 LYS cc_start: 0.7689 (mttt) cc_final: 0.7211 (mtmt) REVERT: B 311 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7456 (mmtt) REVERT: B 461 LYS cc_start: 0.8332 (tptp) cc_final: 0.7659 (ttmm) REVERT: B 530 LYS cc_start: 0.7954 (pttm) cc_final: 0.7112 (mmtt) REVERT: B 588 GLN cc_start: 0.8970 (tt0) cc_final: 0.8662 (tt0) REVERT: B 632 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8202 (ptt90) REVERT: B 650 SER cc_start: 0.6326 (p) cc_final: 0.6109 (p) REVERT: B 655 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7776 (t0) REVERT: B 665 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: B 704 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8536 (t0) REVERT: B 756 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6842 (t) REVERT: B 819 ASP cc_start: 0.7952 (m-30) cc_final: 0.7647 (m-30) REVERT: C 114 MET cc_start: 0.8306 (mmp) cc_final: 0.7666 (ppp) REVERT: C 117 MET cc_start: 0.5742 (mpp) cc_final: 0.5511 (ptp) REVERT: D 131 GLU cc_start: 0.7117 (pt0) cc_final: 0.6757 (mp0) REVERT: D 163 THR cc_start: 0.7857 (p) cc_final: 0.7637 (t) REVERT: D 233 GLU cc_start: 0.8797 (mp0) cc_final: 0.8248 (mp0) REVERT: E 57 SER cc_start: 0.8251 (m) cc_final: 0.7969 (p) REVERT: F 10 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7865 (mm) REVERT: F 65 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8327 (mt0) REVERT: F 68 MET cc_start: 0.7503 (ppp) cc_final: 0.5064 (mmp) REVERT: F 82 PHE cc_start: 0.8593 (p90) cc_final: 0.8172 (p90) REVERT: F 126 ASN cc_start: 0.8422 (t0) cc_final: 0.8015 (t0) REVERT: F 132 ARG cc_start: 0.6723 (mtp85) cc_final: 0.6333 (mtp85) REVERT: G 98 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7539 (tp30) REVERT: H 36 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8323 (tp40) REVERT: I 73 MET cc_start: 0.8227 (tpp) cc_final: 0.7727 (mmt) REVERT: I 208 THR cc_start: 0.8973 (m) cc_final: 0.8646 (p) REVERT: I 238 LEU cc_start: 0.7743 (mt) cc_final: 0.6979 (pp) REVERT: J 87 ILE cc_start: 0.8852 (mp) cc_final: 0.8353 (tt) REVERT: J 95 GLN cc_start: 0.6265 (mt0) cc_final: 0.5912 (pt0) REVERT: J 213 ASN cc_start: 0.7274 (t0) cc_final: 0.7022 (t0) REVERT: K 31 GLN cc_start: 0.8118 (tt0) cc_final: 0.7788 (tp40) outliers start: 78 outliers final: 50 residues processed: 453 average time/residue: 0.1741 time to fit residues: 128.1455 Evaluate side-chains 442 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 81 ILE 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 74 LYS Chi-restraints excluded: chain G residue 99 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 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 177 VAL 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 100 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 280 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 34 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 665 GLN B 669 ASN B 704 ASN B 803 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS H 27 HIS I 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.152307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118937 restraints weight = 50539.769| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.23 r_work: 0.3439 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28471 Z= 0.152 Angle : 0.582 10.955 40228 Z= 0.303 Chirality : 0.039 0.379 4852 Planarity : 0.005 0.064 3725 Dihedral : 20.711 178.499 8400 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.97 % Allowed : 20.69 % Favored : 75.33 % 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: -0.54 (0.17), residues: 2372 helix: 0.92 (0.17), residues: 954 sheet: -0.27 (0.25), residues: 445 loop : -1.70 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 51 TYR 0.023 0.002 TYR D 108 PHE 0.031 0.002 PHE B 740 TRP 0.019 0.001 TRP H 9 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (28468) covalent geometry : angle 0.58185 / 0.30 (40228) hydrogen bonds : bond 0.04242 / 4.56 ( 1006) hydrogen bonds : angle 4.31488 / 5.79 ( 2726) metal coordination : bond 0.00257 / 0.17 ( 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 474 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 387 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8400 (t0) cc_final: 0.7721 (t0) REVERT: B 201 ASN cc_start: 0.7535 (t0) cc_final: 0.7199 (t0) REVERT: B 225 LYS cc_start: 0.7537 (mttt) cc_final: 0.7245 (mtmt) REVERT: B 311 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7538 (mmtt) REVERT: B 461 LYS cc_start: 0.8315 (tptp) cc_final: 0.7705 (ttmm) REVERT: B 530 LYS cc_start: 0.8077 (pttm) cc_final: 0.7311 (mmtt) REVERT: B 588 GLN cc_start: 0.8983 (tt0) cc_final: 0.8705 (tt0) REVERT: B 632 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8097 (ptt90) REVERT: B 650 SER cc_start: 0.6937 (p) cc_final: 0.6674 (p) REVERT: B 655 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 665 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7352 (pp30) REVERT: B 676 ARG cc_start: 0.7161 (ttp80) cc_final: 0.6863 (ppt170) REVERT: B 756 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.7005 (t) REVERT: B 757 PHE cc_start: 0.7330 (t80) cc_final: 0.7049 (t80) REVERT: C 114 MET cc_start: 0.8490 (mmp) cc_final: 0.7817 (ppp) REVERT: D 131 GLU cc_start: 0.7305 (pt0) cc_final: 0.6894 (mp0) REVERT: D 138 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7192 (p0) REVERT: D 163 THR cc_start: 0.7945 (p) cc_final: 0.7717 (t) REVERT: D 233 GLU cc_start: 0.8836 (mp0) cc_final: 0.8454 (mp0) REVERT: E 57 SER cc_start: 0.8345 (m) cc_final: 0.8085 (p) REVERT: E 98 MET cc_start: 0.8647 (ttp) cc_final: 0.8370 (ttm) REVERT: F 10 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7913 (mm) REVERT: F 65 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8277 (mt0) REVERT: F 68 MET cc_start: 0.7432 (ppp) cc_final: 0.4947 (mmp) REVERT: F 82 PHE cc_start: 0.8643 (p90) cc_final: 0.8266 (p90) REVERT: F 126 ASN cc_start: 0.8399 (t0) cc_final: 0.8186 (t0) REVERT: F 132 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6708 (mtp85) REVERT: G 98 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7621 (tp30) REVERT: H 36 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8420 (tp40) REVERT: I 71 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8113 (tm-30) REVERT: I 73 MET cc_start: 0.8207 (tpp) cc_final: 0.7979 (tpp) REVERT: I 208 THR cc_start: 0.9121 (m) cc_final: 0.8779 (p) REVERT: I 238 LEU cc_start: 0.7444 (mt) cc_final: 0.6503 (pp) REVERT: J 87 ILE cc_start: 0.8928 (mp) cc_final: 0.8508 (tt) REVERT: J 95 GLN cc_start: 0.6371 (mt0) cc_final: 0.5966 (pt0) REVERT: J 115 LYS cc_start: 0.6736 (pttm) cc_final: 0.6391 (pttt) REVERT: J 213 ASN cc_start: 0.7382 (t0) cc_final: 0.7128 (t0) REVERT: K 31 GLN cc_start: 0.8150 (tt0) cc_final: 0.7873 (tp40) outliers start: 87 outliers final: 58 residues processed: 442 average time/residue: 0.1759 time to fit residues: 126.4139 Evaluate side-chains 434 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 370 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 665 GLN 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 794 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 54 ARG 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 F residue 10 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 81 ILE 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 74 LYS Chi-restraints excluded: chain G residue 99 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 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 172 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 90 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 99 THR 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: 20.0000 chunk 129 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 704 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 153 HIS I 44 ASN I 143 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113373 restraints weight = 50343.937| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.20 r_work: 0.3345 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 28471 Z= 0.190 Angle : 0.627 11.193 40228 Z= 0.330 Chirality : 0.041 0.373 4852 Planarity : 0.005 0.071 3725 Dihedral : 20.715 179.120 8400 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.11 % Allowed : 20.79 % Favored : 75.10 % 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: 0.87 (0.17), residues: 962 sheet: -0.30 (0.25), residues: 421 loop : -1.69 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 51 TYR 0.021 0.002 TYR B 865 PHE 0.032 0.002 PHE B 740 TRP 0.022 0.002 TRP H 9 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (28468) covalent geometry : angle 0.62708 / 0.33 (40228) hydrogen bonds : bond 0.04663 / 4.99 ( 1006) hydrogen bonds : angle 4.40590 / 5.89 ( 2726) metal coordination : bond 0.00533 / 0.33 ( 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 482 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 392 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8371 (t0) cc_final: 0.7868 (t0) REVERT: B 201 ASN cc_start: 0.7632 (t0) cc_final: 0.7349 (t0) REVERT: B 225 LYS cc_start: 0.7947 (mttt) cc_final: 0.7598 (mtmt) REVERT: B 311 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7559 (mmtt) REVERT: B 461 LYS cc_start: 0.8428 (tptp) cc_final: 0.7913 (ttmt) REVERT: B 588 GLN cc_start: 0.9047 (tt0) cc_final: 0.8769 (tt0) REVERT: B 632 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8338 (ptt90) REVERT: B 650 SER cc_start: 0.7182 (p) cc_final: 0.6927 (p) REVERT: B 655 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (t0) REVERT: B 665 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7687 (pp30) REVERT: B 714 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7601 (tt0) REVERT: B 756 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7705 (t) REVERT: B 757 PHE cc_start: 0.7610 (t80) cc_final: 0.7322 (t80) REVERT: C 114 MET cc_start: 0.8464 (mmp) cc_final: 0.7808 (ppp) REVERT: D 131 GLU cc_start: 0.7269 (pt0) cc_final: 0.6861 (mp0) REVERT: D 163 THR cc_start: 0.8129 (p) cc_final: 0.7914 (t) REVERT: D 233 GLU cc_start: 0.8851 (mp0) cc_final: 0.8447 (mp0) REVERT: D 277 ILE cc_start: 0.7393 (mm) cc_final: 0.7103 (mm) REVERT: E 57 SER cc_start: 0.8530 (m) cc_final: 0.8208 (p) REVERT: E 98 MET cc_start: 0.8615 (ttp) cc_final: 0.8403 (ttm) REVERT: F 10 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7913 (mm) REVERT: F 65 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8277 (mt0) REVERT: F 68 MET cc_start: 0.7352 (ppp) cc_final: 0.4742 (mmp) REVERT: F 82 PHE cc_start: 0.8731 (p90) cc_final: 0.8346 (p90) REVERT: F 132 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7024 (mtp85) REVERT: G 68 MET cc_start: 0.8800 (ptm) cc_final: 0.8511 (ptt) REVERT: H 36 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8368 (tp40) REVERT: H 73 ASP cc_start: 0.8192 (p0) cc_final: 0.7558 (p0) REVERT: I 186 SER cc_start: 0.8789 (m) cc_final: 0.8479 (t) REVERT: J 95 GLN cc_start: 0.6407 (mt0) cc_final: 0.6048 (pt0) REVERT: J 115 LYS cc_start: 0.6688 (pttm) cc_final: 0.6386 (pttt) REVERT: J 213 ASN cc_start: 0.7546 (t0) cc_final: 0.7281 (t0) REVERT: K 134 TYR cc_start: 0.8665 (t80) cc_final: 0.8089 (t80) outliers start: 90 outliers final: 69 residues processed: 450 average time/residue: 0.1789 time to fit residues: 129.5177 Evaluate side-chains 434 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 360 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 666 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 789 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 188 SER 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 33 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS 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 10 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 109 ILE 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 74 LYS Chi-restraints excluded: chain G residue 99 VAL 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 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 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 172 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 90 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 252 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 50.0000 chunk 169 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN B 704 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS I 44 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110079 restraints weight = 50053.958| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.17 r_work: 0.3302 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28471 Z= 0.191 Angle : 0.648 11.543 40228 Z= 0.335 Chirality : 0.042 0.372 4852 Planarity : 0.005 0.068 3725 Dihedral : 20.710 179.566 8400 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.88 % Allowed : 21.70 % Favored : 74.42 % 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: -0.58 (0.17), residues: 2372 helix: 0.92 (0.17), residues: 949 sheet: -0.37 (0.25), residues: 415 loop : -1.68 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 676 TYR 0.020 0.002 TYR E 76 PHE 0.030 0.002 PHE B 740 TRP 0.022 0.002 TRP H 9 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (28468) covalent geometry : angle 0.64791 / 0.34 (40228) hydrogen bonds : bond 0.04687 / 5.01 ( 1006) hydrogen bonds : angle 4.44989 / 5.92 ( 2726) metal coordination : bond 0.00582 / 0.34 ( 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 463 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 378 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8343 (t0) cc_final: 0.7925 (t0) REVERT: B 225 LYS cc_start: 0.8177 (mttt) cc_final: 0.7750 (mtmt) REVERT: B 311 LYS cc_start: 0.8447 (ttpt) cc_final: 0.7678 (mmtt) REVERT: B 588 GLN cc_start: 0.9025 (tt0) cc_final: 0.8815 (tt0) REVERT: B 632 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7266 (pmt100) REVERT: B 650 SER cc_start: 0.7251 (p) cc_final: 0.6963 (p) REVERT: B 655 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7960 (t0) REVERT: B 714 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7651 (tt0) REVERT: B 728 ILE cc_start: 0.9226 (mm) cc_final: 0.8890 (tt) REVERT: C 114 MET cc_start: 0.8412 (mmp) cc_final: 0.7789 (ppp) REVERT: D 1 MET cc_start: 0.8414 (ptm) cc_final: 0.7873 (ppp) REVERT: D 142 MET cc_start: 0.6512 (ttm) cc_final: 0.6306 (ttm) REVERT: D 163 THR cc_start: 0.8309 (p) cc_final: 0.8061 (t) REVERT: D 233 GLU cc_start: 0.8884 (mp0) cc_final: 0.8564 (mp0) REVERT: D 277 ILE cc_start: 0.7405 (mm) cc_final: 0.7146 (mm) REVERT: F 10 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7862 (mm) REVERT: F 65 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8281 (mt0) REVERT: F 68 MET cc_start: 0.7366 (ppp) cc_final: 0.4844 (mmp) REVERT: F 82 PHE cc_start: 0.8789 (p90) cc_final: 0.8374 (p90) REVERT: F 132 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7211 (mtp85) REVERT: G 68 MET cc_start: 0.8823 (ptm) cc_final: 0.8431 (ptt) REVERT: H 73 ASP cc_start: 0.8266 (p0) cc_final: 0.7857 (p0) REVERT: I 73 MET cc_start: 0.8232 (mmm) cc_final: 0.7834 (tpp) REVERT: I 186 SER cc_start: 0.8901 (m) cc_final: 0.8601 (t) REVERT: I 208 THR cc_start: 0.9110 (m) cc_final: 0.8836 (p) REVERT: J 95 GLN cc_start: 0.6290 (mt0) cc_final: 0.6009 (pt0) REVERT: J 213 ASN cc_start: 0.7663 (t0) cc_final: 0.7438 (t0) REVERT: J 240 ASN cc_start: 0.8627 (t0) cc_final: 0.8420 (t0) outliers start: 85 outliers final: 65 residues processed: 430 average time/residue: 0.1768 time to fit residues: 123.2012 Evaluate side-chains 425 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 188 SER 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 54 ARG 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 E residue 126 ILE Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 109 ILE 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 74 LYS 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 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 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 172 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 26 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 112 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 K residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 143 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN I 44 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.146558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112494 restraints weight = 50243.904| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.20 r_work: 0.3339 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28471 Z= 0.125 Angle : 0.618 12.437 40228 Z= 0.319 Chirality : 0.040 0.366 4852 Planarity : 0.005 0.074 3725 Dihedral : 20.715 179.746 8400 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.56 % Allowed : 23.62 % Favored : 73.82 % 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: -0.54 (0.18), residues: 2372 helix: 0.98 (0.17), residues: 962 sheet: -0.48 (0.25), residues: 437 loop : -1.66 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 51 TYR 0.032 0.002 TYR D 108 PHE 0.032 0.002 PHE B 740 TRP 0.021 0.002 TRP H 37 HIS 0.009 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (28468) covalent geometry : angle 0.61834 / 0.32 (40228) hydrogen bonds : bond 0.04154 / 4.40 ( 1006) hydrogen bonds : angle 4.33654 / 5.77 ( 2726) metal coordination : bond 0.00326 / 0.23 ( 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 441 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 385 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8323 (t0) cc_final: 0.7913 (t0) REVERT: B 180 HIS cc_start: 0.5989 (m-70) cc_final: 0.5659 (m-70) REVERT: B 588 GLN cc_start: 0.8994 (tt0) cc_final: 0.8788 (tt0) REVERT: B 632 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8413 (ptt90) REVERT: B 650 SER cc_start: 0.7073 (p) cc_final: 0.6794 (p) REVERT: B 655 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7899 (t0) REVERT: B 714 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7717 (tt0) REVERT: B 728 ILE cc_start: 0.9150 (mm) cc_final: 0.8878 (tt) REVERT: B 828 THR cc_start: 0.8511 (m) cc_final: 0.8032 (m) REVERT: C 43 ILE cc_start: 0.6089 (tt) cc_final: 0.5376 (mp) REVERT: C 44 TRP cc_start: 0.7536 (t-100) cc_final: 0.7266 (t-100) REVERT: C 114 MET cc_start: 0.8403 (mmp) cc_final: 0.7754 (ppp) REVERT: D 1 MET cc_start: 0.8362 (ptm) cc_final: 0.7741 (ppp) REVERT: D 131 GLU cc_start: 0.7137 (pt0) cc_final: 0.6831 (mp0) REVERT: D 163 THR cc_start: 0.8300 (p) cc_final: 0.8048 (t) REVERT: D 197 GLN cc_start: 0.8660 (mt0) cc_final: 0.8458 (mt0) REVERT: D 233 GLU cc_start: 0.8917 (mp0) cc_final: 0.8589 (mp0) REVERT: F 65 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8280 (mt0) REVERT: F 68 MET cc_start: 0.7343 (ppp) cc_final: 0.4854 (mmp) REVERT: F 82 PHE cc_start: 0.8742 (p90) cc_final: 0.8291 (p90) REVERT: F 132 ARG cc_start: 0.7410 (mtp85) cc_final: 0.6993 (mtp85) REVERT: G 68 MET cc_start: 0.8750 (ptm) cc_final: 0.8453 (ptt) REVERT: H 73 ASP cc_start: 0.8195 (p0) cc_final: 0.7799 (p0) REVERT: I 73 MET cc_start: 0.8014 (mmm) cc_final: 0.7497 (mmm) REVERT: I 186 SER cc_start: 0.8821 (m) cc_final: 0.8587 (t) REVERT: I 208 THR cc_start: 0.9126 (m) cc_final: 0.8844 (p) REVERT: J 95 GLN cc_start: 0.6281 (mt0) cc_final: 0.6009 (pt0) REVERT: J 240 ASN cc_start: 0.8511 (t0) cc_final: 0.8229 (t0) outliers start: 56 outliers final: 40 residues processed: 425 average time/residue: 0.1725 time to fit residues: 118.3879 Evaluate side-chains 409 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU 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 655 ASP Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 188 SER 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 54 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 81 ILE 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 74 LYS 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 H residue 86 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 208 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 40.0000 chunk 251 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN J 213 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN K 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110567 restraints weight = 49671.688| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.16 r_work: 0.3302 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 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 = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28471 Z= 0.155 Angle : 0.633 11.592 40228 Z= 0.325 Chirality : 0.040 0.366 4852 Planarity : 0.005 0.069 3725 Dihedral : 20.644 179.550 8400 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.88 % Allowed : 23.66 % Favored : 73.46 % 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: -0.49 (0.18), residues: 2372 helix: 0.99 (0.17), residues: 971 sheet: -0.45 (0.25), residues: 429 loop : -1.62 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 51 TYR 0.028 0.002 TYR D 108 PHE 0.031 0.002 PHE B 740 TRP 0.021 0.002 TRP H 9 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (28468) covalent geometry : angle 0.63264 / 0.33 (40228) hydrogen bonds : bond 0.04364 / 4.67 ( 1006) hydrogen bonds : angle 4.36834 / 5.82 ( 2726) metal coordination : bond 0.00553 / 0.33 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6855.24 seconds wall clock time: 118 minutes 23.70 seconds (7103.70 seconds total)