Starting phenix.real_space_refine on Mon Jun 16 19:06:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.map" model { file = "/net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jau_36134/06_2025/8jau_36134.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 93 5.16 5 C 10893 2.51 5 N 2918 2.21 5 O 3159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17064 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2382 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 1 Chain: "B" 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 401 SG CYS A 54 49.333 59.267 98.815 1.00 24.05 S ATOM 8881 SG CYS B 54 45.488 59.582 98.089 1.00 35.11 S Time building chain proxies: 11.30, per 1000 atoms: 0.66 Number of scatterers: 17064 At special positions: 0 Unit cell: (107.42, 135.3, 202.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 93 16.00 O 3159 8.00 N 2918 7.00 C 10893 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: 3.97 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 5 sheets defined 75.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.786A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.782A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.729A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.906A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.242A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.620A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.954A pdb=" N GLU A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.404A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 4.013A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.532A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.102A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.785A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.756A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.610A pdb=" N HIS A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.532A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 3.624A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 528 removed outlier: 3.736A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.578A pdb=" N VAL A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 4.104A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.630A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.553A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 152 removed outlier: 4.038A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.582A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.716A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.616A pdb=" N PHE E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 230 removed outlier: 3.596A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 3.507A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP E 245 " --> pdb=" O GLY E 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 254 " --> pdb=" O CYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 264 removed outlier: 3.731A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 271 Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.547A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.537A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.973A pdb=" N GLY D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 removed outlier: 4.338A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.638A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.796A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.897A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.569A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 72 No H-bonds generated for 'chain 'B' and resid 71 through 72' Processing helix chain 'B' and resid 73 through 74 No H-bonds generated for 'chain 'B' and resid 73 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.552A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.730A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.252A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.810A pdb=" N TRP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.772A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 241 through 259 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.908A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.648A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 368 removed outlier: 4.319A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.231A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.033A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 489 through 506 Processing helix chain 'B' and resid 507 through 510 removed outlier: 3.731A pdb=" N TYR B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 511 through 528 removed outlier: 4.104A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.532A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.619A pdb=" N GLN G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.185A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.676A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.605A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.752A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 78 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.517A pdb=" N MET I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.034A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.693A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 3.781A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 195 removed outlier: 4.315A pdb=" N TYR I 194 " --> pdb=" O VAL I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 205 Processing helix chain 'I' and resid 207 through 228 removed outlier: 4.186A pdb=" N GLN I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.630A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 271 removed outlier: 3.571A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 289 removed outlier: 3.523A pdb=" N LEU I 278 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE I 286 " --> pdb=" O CYS I 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 298 removed outlier: 5.144A pdb=" N ASN I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR I 298 " --> pdb=" O MET I 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.819A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG C 8 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU C 44 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 51 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 removed outlier: 8.068A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.520A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 32 removed outlier: 7.868A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5569 1.34 - 1.46: 3486 1.46 - 1.58: 8237 1.58 - 1.69: 0 1.69 - 1.81: 139 Bond restraints: 17431 Sorted by residual: bond pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" N MET I 26 " pdb=" CA MET I 26 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 290 " pdb=" CG2 THR A 290 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB THR B 290 " pdb=" CG2 THR B 290 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 17426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 22896 1.37 - 2.73: 506 2.73 - 4.10: 88 4.10 - 5.46: 23 5.46 - 6.83: 4 Bond angle restraints: 23517 Sorted by residual: angle pdb=" C GLU H 54 " pdb=" N ASN H 55 " pdb=" CA ASN H 55 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL H 69 " pdb=" CA VAL H 69 " pdb=" C VAL H 69 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N GLY B 324 " pdb=" CA GLY B 324 " pdb=" C GLY B 324 " ideal model delta sigma weight residual 110.21 113.05 -2.84 9.10e-01 1.21e+00 9.74e+00 angle pdb=" C SER B 552 " pdb=" N VAL B 553 " pdb=" CA VAL B 553 " ideal model delta sigma weight residual 121.97 127.48 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" C GLU E 80 " pdb=" N GLU E 81 " pdb=" CA GLU E 81 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.95e+00 ... (remaining 23512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9447 17.93 - 35.85: 869 35.85 - 53.78: 138 53.78 - 71.71: 30 71.71 - 89.63: 23 Dihedral angle restraints: 10507 sinusoidal: 4304 harmonic: 6203 Sorted by residual: dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N TYR A 222 " pdb=" CA TYR A 222 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N ILE B 304 " pdb=" CA ILE B 304 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " pdb=" CG ASP G 48 " pdb=" OD1 ASP G 48 " ideal model delta sinusoidal sigma weight residual -30.00 -89.95 59.95 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1925 0.043 - 0.086: 552 0.086 - 0.129: 76 0.129 - 0.172: 4 0.172 - 0.215: 1 Chirality restraints: 2558 Sorted by residual: chirality pdb=" CB ILE G 14 " pdb=" CA ILE G 14 " pdb=" CG1 ILE G 14 " pdb=" CG2 ILE G 14 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASN H 55 " pdb=" N ASN H 55 " pdb=" C ASN H 55 " pdb=" CB ASN H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA GLU B 568 " pdb=" N GLU B 568 " pdb=" C GLU B 568 " pdb=" CB GLU B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2555 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS I 255 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO I 256 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 37 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 38 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 49 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 50 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " -0.022 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 744 2.73 - 3.27: 17917 3.27 - 3.81: 29430 3.81 - 4.36: 35752 4.36 - 4.90: 61436 Nonbonded interactions: 145279 Sorted by model distance: nonbonded pdb=" OH TYR I 219 " pdb=" OE1 GLU I 246 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR C 23 " pdb=" OE1 GLU C 26 " model vdw 2.245 3.040 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN B 434 " model vdw 2.282 3.120 nonbonded pdb=" ND2 ASN B 482 " pdb=" O GLY B 519 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG B 103 " pdb=" OH TYR B 107 " model vdw 2.289 3.120 ... (remaining 145274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 8 through 578) } ncs_group { reference = (chain 'C' and resid 2 through 97) selection = (chain 'G' and resid 2 through 97) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 280) } ncs_group { reference = chain 'F' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.960 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.004 0.041 17435 Z= 0.164 Angle : 0.520 6.830 23519 Z= 0.281 Chirality : 0.038 0.215 2558 Planarity : 0.004 0.057 3009 Dihedral : 14.397 89.633 6503 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2072 helix: -0.10 (0.13), residues: 1456 sheet: -1.44 (1.14), residues: 21 loop : -1.79 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.009 0.001 HIS B 410 PHE 0.029 0.002 PHE C 79 TYR 0.020 0.001 TYR A 294 ARG 0.003 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.17340 ( 1076) hydrogen bonds : angle 6.76074 ( 3186) metal coordination : bond 0.00982 ( 4) metal coordination : angle 2.77959 ( 2) covalent geometry : bond 0.00390 (17431) covalent geometry : angle 0.51978 (23517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8132 (m-80) cc_final: 0.7919 (m-80) REVERT: A 445 PHE cc_start: 0.8003 (m-10) cc_final: 0.7747 (m-80) REVERT: E 26 MET cc_start: 0.4846 (ptp) cc_final: 0.4191 (ptp) REVERT: E 82 GLN cc_start: 0.1806 (mm110) cc_final: 0.0675 (tt0) REVERT: E 270 MET cc_start: 0.6431 (tpp) cc_final: 0.6145 (tpp) REVERT: B 9 ILE cc_start: 0.8512 (mp) cc_final: 0.8296 (tp) REVERT: B 451 MET cc_start: 0.7279 (mmt) cc_final: 0.7010 (mmt) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3156 time to fit residues: 128.4719 Evaluate side-chains 194 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A 352 ASN E 36 ASN E 193 GLN E 225 ASN E 274 HIS C 42 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 1 GLN B 38 ASN B 153 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS H 108 ASN I 82 GLN I 116 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129298 restraints weight = 20599.815| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.99 r_work: 0.3168 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17435 Z= 0.164 Angle : 0.508 5.887 23519 Z= 0.277 Chirality : 0.037 0.144 2558 Planarity : 0.004 0.053 3009 Dihedral : 4.155 29.921 2310 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.54 % Allowed : 6.27 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2072 helix: 0.45 (0.13), residues: 1501 sheet: -2.25 (0.74), residues: 40 loop : -1.64 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 279 PHE 0.017 0.001 PHE A 355 TYR 0.016 0.001 TYR A 294 ARG 0.005 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 1076) hydrogen bonds : angle 4.66405 ( 3186) metal coordination : bond 0.01404 ( 4) metal coordination : angle 3.69919 ( 2) covalent geometry : bond 0.00375 (17431) covalent geometry : angle 0.50670 (23517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6348 (tpp) cc_final: 0.6062 (mmt) REVERT: A 359 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7453 (mmm160) REVERT: A 450 GLU cc_start: 0.8020 (tp30) cc_final: 0.7493 (tp30) REVERT: A 565 GLN cc_start: 0.6108 (mp10) cc_final: 0.5738 (mm110) REVERT: E 270 MET cc_start: 0.5743 (tpp) cc_final: 0.5316 (tpp) REVERT: B 9 ILE cc_start: 0.8370 (mp) cc_final: 0.8112 (tp) REVERT: B 302 ASP cc_start: 0.8233 (t0) cc_final: 0.7733 (t0) REVERT: B 392 ASP cc_start: 0.7065 (t0) cc_final: 0.6660 (t0) REVERT: B 445 PHE cc_start: 0.7865 (m-10) cc_final: 0.7554 (m-10) REVERT: B 451 MET cc_start: 0.7174 (mmt) cc_final: 0.6915 (mmt) REVERT: H 59 GLU cc_start: 0.8038 (pp20) cc_final: 0.7829 (pp20) outliers start: 10 outliers final: 6 residues processed: 214 average time/residue: 0.2969 time to fit residues: 97.5274 Evaluate side-chains 196 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 566 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS H 108 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127898 restraints weight = 20508.885| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.96 r_work: 0.3258 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17435 Z= 0.188 Angle : 0.503 7.034 23519 Z= 0.270 Chirality : 0.038 0.141 2558 Planarity : 0.004 0.055 3009 Dihedral : 4.135 32.341 2310 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.35 % Allowed : 8.60 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2072 helix: 0.60 (0.13), residues: 1499 sheet: -2.15 (0.75), residues: 40 loop : -1.59 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.001 HIS A 410 PHE 0.016 0.002 PHE A 355 TYR 0.019 0.001 TYR A 294 ARG 0.005 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1076) hydrogen bonds : angle 4.40923 ( 3186) metal coordination : bond 0.01390 ( 4) metal coordination : angle 4.99724 ( 2) covalent geometry : bond 0.00444 (17431) covalent geometry : angle 0.50085 (23517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 2.349 Fit side-chains REVERT: A 156 MET cc_start: 0.6370 (tpp) cc_final: 0.6016 (mmt) REVERT: A 160 PHE cc_start: 0.8250 (m-80) cc_final: 0.7935 (m-80) REVERT: A 358 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 359 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7455 (mmm160) REVERT: A 445 PHE cc_start: 0.8051 (m-10) cc_final: 0.7026 (m-10) REVERT: A 450 GLU cc_start: 0.8037 (tp30) cc_final: 0.7543 (tp30) REVERT: A 565 GLN cc_start: 0.6006 (mp10) cc_final: 0.5705 (mm110) REVERT: E 75 ARG cc_start: 0.7333 (tpp80) cc_final: 0.7117 (ttp-170) REVERT: E 194 TYR cc_start: 0.6287 (p90) cc_final: 0.6020 (p90) REVERT: C 55 LYS cc_start: 0.7780 (pttt) cc_final: 0.7472 (pttm) REVERT: B 9 ILE cc_start: 0.8446 (mp) cc_final: 0.8196 (tp) REVERT: B 387 GLU cc_start: 0.7688 (tt0) cc_final: 0.7471 (tt0) REVERT: B 443 ARG cc_start: 0.7851 (mmt180) cc_final: 0.7565 (mmt180) REVERT: B 445 PHE cc_start: 0.7754 (m-10) cc_final: 0.7372 (m-10) REVERT: B 451 MET cc_start: 0.7212 (mmt) cc_final: 0.6933 (mmt) REVERT: B 568 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: H 59 GLU cc_start: 0.8184 (pp20) cc_final: 0.7908 (pp20) REVERT: I 222 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6792 (tm-30) REVERT: I 248 ILE cc_start: 0.8695 (mm) cc_final: 0.8435 (tt) outliers start: 25 outliers final: 18 residues processed: 216 average time/residue: 0.3328 time to fit residues: 109.0435 Evaluate side-chains 207 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 73 optimal weight: 0.0770 chunk 115 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 176 optimal weight: 0.5980 chunk 84 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 199 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN G 10 HIS I 156 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131435 restraints weight = 20369.390| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17435 Z= 0.112 Angle : 0.449 6.363 23519 Z= 0.243 Chirality : 0.035 0.144 2558 Planarity : 0.004 0.052 3009 Dihedral : 4.003 30.425 2310 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.14 % Allowed : 10.44 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2072 helix: 0.85 (0.14), residues: 1513 sheet: -2.03 (0.76), residues: 40 loop : -1.53 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.001 HIS A 89 PHE 0.013 0.001 PHE E 64 TYR 0.017 0.001 TYR E 253 ARG 0.005 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1076) hydrogen bonds : angle 4.21340 ( 3186) metal coordination : bond 0.00846 ( 4) metal coordination : angle 4.54604 ( 2) covalent geometry : bond 0.00239 (17431) covalent geometry : angle 0.44670 (23517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6411 (tpp) cc_final: 0.6020 (mmt) REVERT: A 160 PHE cc_start: 0.8180 (m-80) cc_final: 0.7811 (m-80) REVERT: A 445 PHE cc_start: 0.8005 (m-10) cc_final: 0.6978 (m-10) REVERT: A 450 GLU cc_start: 0.7997 (tp30) cc_final: 0.7680 (tp30) REVERT: A 565 GLN cc_start: 0.5914 (mp10) cc_final: 0.5583 (mm110) REVERT: E 75 ARG cc_start: 0.7348 (tpp80) cc_final: 0.7147 (ttp-170) REVERT: E 148 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6850 (ttp80) REVERT: D 17 MET cc_start: 0.7167 (ptt) cc_final: 0.6802 (ttp) REVERT: B 9 ILE cc_start: 0.8381 (mp) cc_final: 0.8146 (tp) REVERT: B 443 ARG cc_start: 0.7860 (mmt180) cc_final: 0.7611 (mmt180) REVERT: B 446 LYS cc_start: 0.8449 (tptm) cc_final: 0.8149 (tptt) REVERT: B 451 MET cc_start: 0.7112 (mmt) cc_final: 0.6906 (mmt) REVERT: G 6 MET cc_start: 0.8744 (ttp) cc_final: 0.8484 (ttt) REVERT: H 59 GLU cc_start: 0.7986 (pp20) cc_final: 0.7662 (pp20) REVERT: I 222 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6746 (tm-30) REVERT: I 248 ILE cc_start: 0.8637 (mm) cc_final: 0.8417 (tt) outliers start: 21 outliers final: 15 residues processed: 216 average time/residue: 0.3875 time to fit residues: 128.2772 Evaluate side-chains 207 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 53 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 118 optimal weight: 0.0980 chunk 179 optimal weight: 0.0040 chunk 165 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 0.0470 chunk 90 optimal weight: 0.0570 chunk 203 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.0808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS I 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.171825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134149 restraints weight = 20449.761| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.94 r_work: 0.3372 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17435 Z= 0.096 Angle : 0.432 6.050 23519 Z= 0.235 Chirality : 0.035 0.143 2558 Planarity : 0.003 0.050 3009 Dihedral : 3.856 26.267 2310 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.19 % Allowed : 11.63 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2072 helix: 1.05 (0.14), residues: 1514 sheet: -1.81 (0.76), residues: 42 loop : -1.42 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.000 HIS A 89 PHE 0.013 0.001 PHE E 64 TYR 0.023 0.001 TYR B 495 ARG 0.006 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1076) hydrogen bonds : angle 4.04536 ( 3186) metal coordination : bond 0.00602 ( 4) metal coordination : angle 4.11370 ( 2) covalent geometry : bond 0.00190 (17431) covalent geometry : angle 0.43083 (23517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6516 (tpp) cc_final: 0.6118 (mmt) REVERT: A 160 PHE cc_start: 0.8183 (m-80) cc_final: 0.7811 (m-80) REVERT: A 445 PHE cc_start: 0.7865 (m-10) cc_final: 0.6939 (m-10) REVERT: A 450 GLU cc_start: 0.7964 (tp30) cc_final: 0.7692 (tp30) REVERT: A 565 GLN cc_start: 0.5848 (mp10) cc_final: 0.5554 (mm110) REVERT: E 75 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7123 (mtm-85) REVERT: D 17 MET cc_start: 0.7248 (ptt) cc_final: 0.6978 (ttp) REVERT: B 392 ASP cc_start: 0.7067 (t0) cc_final: 0.6863 (t0) REVERT: B 446 LYS cc_start: 0.8483 (tptm) cc_final: 0.8156 (tptt) REVERT: H 59 GLU cc_start: 0.7849 (pp20) cc_final: 0.7055 (pp20) REVERT: I 195 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8283 (mtpp) REVERT: I 222 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6745 (tm-30) REVERT: I 248 ILE cc_start: 0.8618 (mm) cc_final: 0.8417 (tt) outliers start: 22 outliers final: 13 residues processed: 222 average time/residue: 0.2785 time to fit residues: 94.5498 Evaluate side-chains 207 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 333 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN D 85 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127520 restraints weight = 20596.122| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.02 r_work: 0.3266 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17435 Z= 0.169 Angle : 0.483 7.740 23519 Z= 0.258 Chirality : 0.038 0.211 2558 Planarity : 0.003 0.051 3009 Dihedral : 3.922 25.066 2310 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.19 % Allowed : 12.76 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2072 helix: 0.98 (0.14), residues: 1512 sheet: -1.81 (0.78), residues: 42 loop : -1.50 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 147 HIS 0.006 0.001 HIS A 279 PHE 0.015 0.001 PHE B 445 TYR 0.027 0.001 TYR E 253 ARG 0.011 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1076) hydrogen bonds : angle 4.10570 ( 3186) metal coordination : bond 0.01144 ( 4) metal coordination : angle 4.41238 ( 2) covalent geometry : bond 0.00397 (17431) covalent geometry : angle 0.48082 (23517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6535 (tpp) cc_final: 0.6080 (mmt) REVERT: A 160 PHE cc_start: 0.8285 (m-80) cc_final: 0.7924 (m-80) REVERT: A 445 PHE cc_start: 0.8101 (m-10) cc_final: 0.7113 (m-10) REVERT: A 565 GLN cc_start: 0.5989 (mp10) cc_final: 0.5660 (mm110) REVERT: B 446 LYS cc_start: 0.8501 (tptm) cc_final: 0.8161 (tptt) REVERT: B 484 ASP cc_start: 0.7594 (m-30) cc_final: 0.7201 (m-30) REVERT: H 59 GLU cc_start: 0.8032 (pp20) cc_final: 0.7697 (pp20) REVERT: H 111 ASP cc_start: 0.8435 (t0) cc_final: 0.8011 (t0) REVERT: I 26 MET cc_start: 0.7755 (ptt) cc_final: 0.7406 (ptt) REVERT: I 195 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8296 (mtpp) REVERT: I 222 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6746 (tm-30) REVERT: I 248 ILE cc_start: 0.8695 (mm) cc_final: 0.8486 (tt) outliers start: 22 outliers final: 16 residues processed: 207 average time/residue: 0.2961 time to fit residues: 93.7890 Evaluate side-chains 200 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 138 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 279 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130423 restraints weight = 20355.154| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.94 r_work: 0.3308 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17435 Z= 0.134 Angle : 0.472 9.302 23519 Z= 0.250 Chirality : 0.036 0.187 2558 Planarity : 0.004 0.063 3009 Dihedral : 3.916 24.604 2310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.46 % Allowed : 12.87 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 2072 helix: 1.04 (0.14), residues: 1510 sheet: -1.81 (0.77), residues: 42 loop : -1.48 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.005 0.001 HIS C 10 PHE 0.019 0.001 PHE B 445 TYR 0.031 0.001 TYR E 253 ARG 0.007 0.000 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1076) hydrogen bonds : angle 4.04751 ( 3186) metal coordination : bond 0.01028 ( 4) metal coordination : angle 4.53221 ( 2) covalent geometry : bond 0.00309 (17431) covalent geometry : angle 0.47028 (23517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8347 (m-30) cc_final: 0.8038 (m-30) REVERT: A 156 MET cc_start: 0.6501 (tpp) cc_final: 0.6046 (mmt) REVERT: A 160 PHE cc_start: 0.8277 (m-80) cc_final: 0.7914 (m-80) REVERT: A 445 PHE cc_start: 0.8016 (m-10) cc_final: 0.7095 (m-10) REVERT: A 565 GLN cc_start: 0.5991 (mp10) cc_final: 0.5741 (mm110) REVERT: C 55 LYS cc_start: 0.7713 (pttt) cc_final: 0.7250 (pttm) REVERT: B 446 LYS cc_start: 0.8475 (tptm) cc_final: 0.8116 (tptt) REVERT: G 6 MET cc_start: 0.8817 (ttp) cc_final: 0.8503 (ttt) REVERT: H 59 GLU cc_start: 0.8046 (pp20) cc_final: 0.7687 (pp20) REVERT: H 111 ASP cc_start: 0.8380 (t0) cc_final: 0.7982 (t0) REVERT: I 26 MET cc_start: 0.7769 (ptt) cc_final: 0.7448 (ptt) REVERT: I 195 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8256 (mtpp) REVERT: I 222 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6739 (tm-30) outliers start: 27 outliers final: 19 residues processed: 212 average time/residue: 0.2883 time to fit residues: 94.1793 Evaluate side-chains 206 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 163 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130306 restraints weight = 20238.662| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.93 r_work: 0.3332 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17435 Z= 0.128 Angle : 0.471 8.440 23519 Z= 0.249 Chirality : 0.037 0.189 2558 Planarity : 0.004 0.053 3009 Dihedral : 3.931 23.670 2310 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.35 % Allowed : 13.25 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2072 helix: 1.05 (0.13), residues: 1509 sheet: -1.83 (0.76), residues: 42 loop : -1.45 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS A 279 PHE 0.023 0.001 PHE B 445 TYR 0.036 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1076) hydrogen bonds : angle 4.04909 ( 3186) metal coordination : bond 0.00931 ( 4) metal coordination : angle 4.54427 ( 2) covalent geometry : bond 0.00291 (17431) covalent geometry : angle 0.46902 (23517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8302 (m-30) cc_final: 0.7974 (m-30) REVERT: A 156 MET cc_start: 0.6447 (tpp) cc_final: 0.5992 (mmt) REVERT: A 160 PHE cc_start: 0.8175 (m-80) cc_final: 0.7780 (m-80) REVERT: A 445 PHE cc_start: 0.7965 (m-10) cc_final: 0.7043 (m-10) REVERT: A 565 GLN cc_start: 0.5977 (mp10) cc_final: 0.5664 (mm110) REVERT: C 55 LYS cc_start: 0.7674 (pttt) cc_final: 0.7210 (pttm) REVERT: B 446 LYS cc_start: 0.8442 (tptm) cc_final: 0.8056 (tptt) REVERT: G 6 MET cc_start: 0.8760 (ttp) cc_final: 0.8459 (ttt) REVERT: H 59 GLU cc_start: 0.7987 (pp20) cc_final: 0.7615 (pp20) REVERT: H 111 ASP cc_start: 0.8385 (t0) cc_final: 0.7977 (t0) REVERT: I 195 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8222 (mtpp) REVERT: I 222 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6699 (tm-30) outliers start: 25 outliers final: 24 residues processed: 209 average time/residue: 0.2850 time to fit residues: 90.8441 Evaluate side-chains 211 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129015 restraints weight = 20503.532| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.96 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17435 Z= 0.163 Angle : 0.509 13.844 23519 Z= 0.265 Chirality : 0.038 0.203 2558 Planarity : 0.004 0.049 3009 Dihedral : 3.983 25.418 2310 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.62 % Allowed : 13.41 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2072 helix: 0.97 (0.13), residues: 1508 sheet: -1.89 (0.76), residues: 42 loop : -1.50 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 147 HIS 0.006 0.001 HIS E 88 PHE 0.016 0.001 PHE B 445 TYR 0.017 0.001 TYR A 488 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1076) hydrogen bonds : angle 4.08839 ( 3186) metal coordination : bond 0.01126 ( 4) metal coordination : angle 4.72462 ( 2) covalent geometry : bond 0.00384 (17431) covalent geometry : angle 0.50749 (23517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8405 (m-30) cc_final: 0.8092 (m-30) REVERT: A 156 MET cc_start: 0.6428 (tpp) cc_final: 0.5973 (mmt) REVERT: A 160 PHE cc_start: 0.8277 (m-80) cc_final: 0.7895 (m-80) REVERT: A 359 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7452 (mmm160) REVERT: A 445 PHE cc_start: 0.8021 (m-10) cc_final: 0.7147 (m-10) REVERT: A 565 GLN cc_start: 0.6030 (mp10) cc_final: 0.5756 (mm110) REVERT: E 186 ASN cc_start: 0.8103 (t0) cc_final: 0.7668 (m110) REVERT: C 43 ARG cc_start: 0.8020 (ptp-170) cc_final: 0.7468 (ptp90) REVERT: B 446 LYS cc_start: 0.8442 (tptm) cc_final: 0.8064 (tptt) REVERT: G 6 MET cc_start: 0.8822 (ttp) cc_final: 0.8609 (ttt) REVERT: H 59 GLU cc_start: 0.8156 (pp20) cc_final: 0.7759 (pp20) REVERT: H 111 ASP cc_start: 0.8506 (t0) cc_final: 0.8116 (t0) REVERT: I 195 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8266 (mtpp) REVERT: I 222 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6654 (tm-30) outliers start: 30 outliers final: 24 residues processed: 212 average time/residue: 0.3334 time to fit residues: 109.2057 Evaluate side-chains 212 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 156 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 306 GLN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129298 restraints weight = 20394.425| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17435 Z= 0.153 Angle : 0.501 12.774 23519 Z= 0.263 Chirality : 0.037 0.202 2558 Planarity : 0.004 0.056 3009 Dihedral : 3.974 25.983 2310 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 14.12 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2072 helix: 1.00 (0.13), residues: 1506 sheet: -1.88 (0.75), residues: 42 loop : -1.50 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS E 88 PHE 0.022 0.001 PHE C 79 TYR 0.031 0.001 TYR E 253 ARG 0.009 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1076) hydrogen bonds : angle 4.07466 ( 3186) metal coordination : bond 0.01106 ( 4) metal coordination : angle 4.82074 ( 2) covalent geometry : bond 0.00360 (17431) covalent geometry : angle 0.49951 (23517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8406 (m-30) cc_final: 0.8090 (m-30) REVERT: A 156 MET cc_start: 0.6420 (tpp) cc_final: 0.5965 (mmt) REVERT: A 160 PHE cc_start: 0.8273 (m-80) cc_final: 0.7912 (m-80) REVERT: A 359 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7441 (mmm160) REVERT: A 565 GLN cc_start: 0.6048 (mp10) cc_final: 0.5785 (mm110) REVERT: E 186 ASN cc_start: 0.8113 (t0) cc_final: 0.7681 (m110) REVERT: C 55 LYS cc_start: 0.7598 (pttt) cc_final: 0.7194 (pttm) REVERT: B 446 LYS cc_start: 0.8427 (tptm) cc_final: 0.8039 (tptt) REVERT: H 59 GLU cc_start: 0.8164 (pp20) cc_final: 0.7762 (pp20) REVERT: H 111 ASP cc_start: 0.8504 (t0) cc_final: 0.8124 (t0) REVERT: I 195 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8249 (mtpp) REVERT: I 222 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6663 (tm-30) outliers start: 24 outliers final: 22 residues processed: 210 average time/residue: 0.3474 time to fit residues: 112.2910 Evaluate side-chains 210 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129490 restraints weight = 20384.389| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.94 r_work: 0.3311 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17435 Z= 0.147 Angle : 0.501 13.145 23519 Z= 0.262 Chirality : 0.037 0.199 2558 Planarity : 0.004 0.054 3009 Dihedral : 3.962 25.551 2310 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.30 % Allowed : 14.28 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 2072 helix: 1.02 (0.13), residues: 1506 sheet: -1.85 (0.77), residues: 42 loop : -1.52 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.005 0.001 HIS E 88 PHE 0.013 0.001 PHE B 101 TYR 0.028 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1076) hydrogen bonds : angle 4.05926 ( 3186) metal coordination : bond 0.01065 ( 4) metal coordination : angle 4.82237 ( 2) covalent geometry : bond 0.00343 (17431) covalent geometry : angle 0.49882 (23517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11247.53 seconds wall clock time: 198 minutes 57.63 seconds (11937.63 seconds total)