Starting phenix.real_space_refine on Mon May 19 20:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jau_36134/05_2025/8jau_36134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jau_36134/05_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_36134/05_2025/8jau_36134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jau_36134/05_2025/8jau_36134.map" model { file = "/net/cci-nas-00/data/ceres_data/8jau_36134/05_2025/8jau_36134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jau_36134/05_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-5687/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: 10.75, per 1000 atoms: 0.63 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: 4.12 Conformation dependent library (CDL) restraints added in 2.0 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: 1.64 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: 4.73 Time building geometry restraints manager: 4.74 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: 6.600 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.190 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.130 ------------------------------------------------------------------------------- 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 : 1.770 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: 0.3117 time to fit residues: 126.8107 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 : 1.771 ------------------------------------------------------------------------------- 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 = 0.129295 restraints weight = 20599.876| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.99 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- 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 5.888 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 3.69904 ( 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 : 1.876 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6350 (tpp) cc_final: 0.6064 (mmt) REVERT: A 359 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7453 (mmm160) REVERT: A 450 GLU cc_start: 0.8019 (tp30) cc_final: 0.7493 (tp30) REVERT: A 565 GLN cc_start: 0.6111 (mp10) cc_final: 0.5741 (mm110) REVERT: E 270 MET cc_start: 0.5710 (tpp) cc_final: 0.5282 (tpp) REVERT: B 9 ILE cc_start: 0.8372 (mp) cc_final: 0.8114 (tp) REVERT: B 302 ASP cc_start: 0.8233 (t0) cc_final: 0.7733 (t0) REVERT: B 392 ASP cc_start: 0.7066 (t0) cc_final: 0.6661 (t0) REVERT: B 445 PHE cc_start: 0.7863 (m-10) cc_final: 0.7552 (m-10) REVERT: B 451 MET cc_start: 0.7172 (mmt) cc_final: 0.6913 (mmt) REVERT: H 59 GLU cc_start: 0.8035 (pp20) cc_final: 0.7826 (pp20) outliers start: 10 outliers final: 6 residues processed: 214 average time/residue: 0.3019 time to fit residues: 99.4270 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 : 1.931 ------------------------------------------------------------------------------- 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: 0.0970 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 I 156 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.168033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129594 restraints weight = 20505.486| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.97 r_work: 0.3313 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.145 Angle : 0.473 6.228 23519 Z= 0.255 Chirality : 0.036 0.144 2558 Planarity : 0.004 0.053 3009 Dihedral : 4.060 31.384 2310 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 8.60 % Favored : 90.27 % 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: 0.05 (0.18), residues: 2072 helix: 0.71 (0.13), residues: 1502 sheet: -2.09 (0.75), residues: 40 loop : -1.60 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.001 HIS A 452 PHE 0.015 0.001 PHE A 355 TYR 0.015 0.001 TYR A 294 ARG 0.006 0.000 ARG G 8 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 1076) hydrogen bonds : angle 4.34786 ( 3186) metal coordination : bond 0.01002 ( 4) metal coordination : angle 4.42004 ( 2) covalent geometry : bond 0.00333 (17431) covalent geometry : angle 0.47097 (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 225 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6407 (tpp) cc_final: 0.6043 (mmt) REVERT: A 160 PHE cc_start: 0.8216 (m-80) cc_final: 0.7892 (m-80) REVERT: A 445 PHE cc_start: 0.7955 (m-10) cc_final: 0.6977 (m-10) REVERT: A 450 GLU cc_start: 0.8024 (tp30) cc_final: 0.7520 (tp30) REVERT: A 565 GLN cc_start: 0.6007 (mp10) cc_final: 0.5723 (mm110) REVERT: E 75 ARG cc_start: 0.7397 (tpp80) cc_final: 0.7153 (ttp-170) REVERT: E 194 TYR cc_start: 0.6323 (p90) cc_final: 0.6032 (p90) REVERT: E 221 GLN cc_start: 0.8003 (tp40) cc_final: 0.7722 (tp40) REVERT: E 253 TYR cc_start: 0.5058 (m-10) cc_final: 0.4500 (m-10) REVERT: C 55 LYS cc_start: 0.7758 (pttt) cc_final: 0.7427 (pttm) REVERT: B 9 ILE cc_start: 0.8405 (mp) cc_final: 0.8162 (tp) REVERT: B 387 GLU cc_start: 0.7660 (tt0) cc_final: 0.7411 (tt0) REVERT: B 443 ARG cc_start: 0.7879 (mmt180) cc_final: 0.7636 (mmt180) REVERT: B 445 PHE cc_start: 0.7683 (m-10) cc_final: 0.7263 (m-10) REVERT: B 451 MET cc_start: 0.7152 (mmt) cc_final: 0.6939 (mmt) REVERT: H 59 GLU cc_start: 0.8041 (pp20) cc_final: 0.7766 (pp20) REVERT: I 222 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6797 (tm-30) REVERT: I 248 ILE cc_start: 0.8670 (mm) cc_final: 0.8425 (tt) outliers start: 21 outliers final: 13 residues processed: 216 average time/residue: 0.2827 time to fit residues: 92.9729 Evaluate side-chains 202 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 373 LEU Chi-restraints excluded: chain A residue 537 HIS 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 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain G residue 35 LEU 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: 0.6980 chunk 115 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 84 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130163 restraints weight = 20479.373| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.94 r_work: 0.3337 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17435 Z= 0.130 Angle : 0.455 6.335 23519 Z= 0.246 Chirality : 0.036 0.142 2558 Planarity : 0.004 0.051 3009 Dihedral : 4.000 29.743 2310 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.24 % Allowed : 10.22 % Favored : 88.53 % 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: 0.24 (0.19), residues: 2072 helix: 0.85 (0.14), residues: 1508 sheet: -2.05 (0.76), residues: 40 loop : -1.55 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS A 89 PHE 0.013 0.001 PHE E 64 TYR 0.015 0.001 TYR A 488 ARG 0.005 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1076) hydrogen bonds : angle 4.21794 ( 3186) metal coordination : bond 0.00991 ( 4) metal coordination : angle 4.45886 ( 2) covalent geometry : bond 0.00294 (17431) covalent geometry : angle 0.45289 (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 224 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6380 (tpp) cc_final: 0.5982 (mmt) REVERT: A 160 PHE cc_start: 0.8213 (m-80) cc_final: 0.7847 (m-80) REVERT: A 445 PHE cc_start: 0.8033 (m-10) cc_final: 0.7012 (m-10) REVERT: A 450 GLU cc_start: 0.8002 (tp30) cc_final: 0.7702 (tp30) REVERT: A 565 GLN cc_start: 0.5895 (mp10) cc_final: 0.5577 (mm110) REVERT: E 148 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6880 (ttp80) REVERT: B 9 ILE cc_start: 0.8378 (mp) cc_final: 0.8144 (tp) REVERT: B 443 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7637 (mmt180) REVERT: B 446 LYS cc_start: 0.8491 (tptm) cc_final: 0.8182 (tptt) REVERT: B 451 MET cc_start: 0.7168 (mmt) cc_final: 0.6937 (mmt) REVERT: G 6 MET cc_start: 0.8755 (ttp) cc_final: 0.8492 (ttt) REVERT: H 59 GLU cc_start: 0.8014 (pp20) cc_final: 0.7680 (pp20) REVERT: I 26 MET cc_start: 0.7742 (ptt) cc_final: 0.7387 (ptt) REVERT: I 49 TYR cc_start: 0.8005 (t80) cc_final: 0.7799 (t80) REVERT: I 222 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6752 (tm-30) REVERT: I 248 ILE cc_start: 0.8697 (mm) cc_final: 0.8467 (tt) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.3040 time to fit residues: 98.0358 Evaluate side-chains 205 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 223 ASP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 53 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 118 optimal weight: 0.0870 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 D 85 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129233 restraints weight = 20533.113| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.96 r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17435 Z= 0.155 Angle : 0.465 6.667 23519 Z= 0.250 Chirality : 0.037 0.139 2558 Planarity : 0.004 0.050 3009 Dihedral : 3.980 28.253 2310 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.51 % Allowed : 11.14 % Favored : 87.34 % 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: 0.27 (0.19), residues: 2072 helix: 0.87 (0.14), residues: 1506 sheet: -2.05 (0.77), residues: 40 loop : -1.54 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS A 89 PHE 0.017 0.001 PHE C 79 TYR 0.022 0.001 TYR A 488 ARG 0.006 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1076) hydrogen bonds : angle 4.17775 ( 3186) metal coordination : bond 0.01144 ( 4) metal coordination : angle 4.78388 ( 2) covalent geometry : bond 0.00361 (17431) covalent geometry : angle 0.46316 (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 229 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.913 Fit side-chains REVERT: A 156 MET cc_start: 0.6399 (tpp) cc_final: 0.5975 (mmt) REVERT: A 160 PHE cc_start: 0.8200 (m-80) cc_final: 0.7834 (m-80) REVERT: A 358 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 359 ARG cc_start: 0.7844 (mtt-85) cc_final: 0.7387 (mmm160) REVERT: A 445 PHE cc_start: 0.7982 (m-10) cc_final: 0.6940 (m-10) REVERT: A 450 GLU cc_start: 0.8016 (tp30) cc_final: 0.7678 (tp30) REVERT: A 565 GLN cc_start: 0.5890 (mp10) cc_final: 0.5607 (mm110) REVERT: C 55 LYS cc_start: 0.7731 (pttt) cc_final: 0.7447 (pttm) REVERT: B 9 ILE cc_start: 0.8380 (mp) cc_final: 0.8143 (tp) REVERT: B 392 ASP cc_start: 0.7123 (t0) cc_final: 0.6838 (t0) REVERT: B 446 LYS cc_start: 0.8519 (tptm) cc_final: 0.8182 (tptt) REVERT: B 451 MET cc_start: 0.7096 (mmt) cc_final: 0.6856 (mmt) REVERT: H 59 GLU cc_start: 0.8089 (pp20) cc_final: 0.7729 (pp20) REVERT: I 222 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6739 (tm-30) REVERT: I 248 ILE cc_start: 0.8645 (mm) cc_final: 0.8434 (tt) outliers start: 28 outliers final: 23 residues processed: 215 average time/residue: 0.2887 time to fit residues: 95.2059 Evaluate side-chains 212 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 266 GLU 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 6 MET Chi-restraints excluded: chain C residue 75 VAL 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 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 G residue 14 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS I 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130304 restraints weight = 20457.141| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.95 r_work: 0.3325 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17435 Z= 0.130 Angle : 0.458 6.584 23519 Z= 0.246 Chirality : 0.036 0.139 2558 Planarity : 0.003 0.049 3009 Dihedral : 3.946 26.823 2310 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.57 % Allowed : 12.11 % Favored : 86.32 % 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: 0.39 (0.19), residues: 2072 helix: 0.96 (0.14), residues: 1510 sheet: -1.96 (0.78), residues: 42 loop : -1.51 (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 A 279 PHE 0.018 0.001 PHE B 445 TYR 0.031 0.001 TYR E 253 ARG 0.006 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1076) hydrogen bonds : angle 4.11842 ( 3186) metal coordination : bond 0.00980 ( 4) metal coordination : angle 4.73619 ( 2) covalent geometry : bond 0.00294 (17431) covalent geometry : angle 0.45591 (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 229 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6417 (tpp) cc_final: 0.5988 (mmt) REVERT: A 160 PHE cc_start: 0.8180 (m-80) cc_final: 0.7806 (m-80) REVERT: A 450 GLU cc_start: 0.8014 (tp30) cc_final: 0.7758 (tp30) REVERT: A 565 GLN cc_start: 0.5917 (mp10) cc_final: 0.5562 (mm110) REVERT: E 270 MET cc_start: 0.5731 (tpp) cc_final: 0.5055 (tpp) REVERT: B 9 ILE cc_start: 0.8371 (mp) cc_final: 0.8141 (tp) REVERT: B 392 ASP cc_start: 0.7097 (t0) cc_final: 0.6885 (t0) REVERT: B 445 PHE cc_start: 0.7602 (m-10) cc_final: 0.7342 (m-80) REVERT: B 446 LYS cc_start: 0.8496 (tptm) cc_final: 0.8135 (tptt) REVERT: B 451 MET cc_start: 0.7077 (mmt) cc_final: 0.6841 (mmt) REVERT: H 59 GLU cc_start: 0.8036 (pp20) cc_final: 0.7681 (pp20) REVERT: I 195 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8240 (mtpp) REVERT: I 222 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6732 (tm-30) REVERT: I 248 ILE cc_start: 0.8583 (mm) cc_final: 0.8383 (tt) outliers start: 29 outliers final: 22 residues processed: 217 average time/residue: 0.2890 time to fit residues: 96.1341 Evaluate side-chains 207 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 266 GLU 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 E residue 254 LEU Chi-restraints excluded: chain C residue 75 VAL 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 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 14 ILE 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: 0.8980 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 138 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 333 HIS A 529 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 = 0.3997 r_free = 0.3997 target = 0.167712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129051 restraints weight = 20488.488| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.95 r_work: 0.3330 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17435 Z= 0.156 Angle : 0.473 6.783 23519 Z= 0.253 Chirality : 0.037 0.161 2558 Planarity : 0.004 0.048 3009 Dihedral : 3.967 25.687 2310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.89 % Allowed : 12.28 % Favored : 85.83 % 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: 0.37 (0.19), residues: 2072 helix: 0.94 (0.14), residues: 1506 sheet: -1.99 (0.77), residues: 42 loop : -1.48 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.004 0.001 HIS C 10 PHE 0.018 0.001 PHE B 445 TYR 0.029 0.001 TYR E 253 ARG 0.007 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1076) hydrogen bonds : angle 4.11366 ( 3186) metal coordination : bond 0.01115 ( 4) metal coordination : angle 4.90694 ( 2) covalent geometry : bond 0.00366 (17431) covalent geometry : angle 0.47097 (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 228 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6445 (tpp) cc_final: 0.5991 (mmt) REVERT: A 160 PHE cc_start: 0.8203 (m-80) cc_final: 0.7827 (m-80) REVERT: A 450 GLU cc_start: 0.8029 (tp30) cc_final: 0.7778 (tp30) REVERT: A 565 GLN cc_start: 0.6002 (mp10) cc_final: 0.5724 (mm110) REVERT: E 270 MET cc_start: 0.5810 (tpp) cc_final: 0.5133 (tpp) REVERT: C 55 LYS cc_start: 0.7706 (pttt) cc_final: 0.7239 (pttm) REVERT: B 9 ILE cc_start: 0.8419 (mp) cc_final: 0.8189 (tp) REVERT: B 188 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (tt) REVERT: B 445 PHE cc_start: 0.7467 (m-10) cc_final: 0.7207 (m-10) REVERT: B 446 LYS cc_start: 0.8503 (tptm) cc_final: 0.8127 (tptt) REVERT: B 451 MET cc_start: 0.7088 (mmt) cc_final: 0.6818 (mmt) REVERT: G 6 MET cc_start: 0.8843 (ttp) cc_final: 0.8538 (ttt) REVERT: H 59 GLU cc_start: 0.8101 (pp20) cc_final: 0.7700 (pp20) REVERT: I 195 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8239 (mtpp) REVERT: I 222 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6682 (tm-30) REVERT: I 248 ILE cc_start: 0.8640 (mm) cc_final: 0.8428 (tt) outliers start: 35 outliers final: 29 residues processed: 216 average time/residue: 0.2818 time to fit residues: 94.2892 Evaluate side-chains 215 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 266 GLU 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 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 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 246 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 566 SER Chi-restraints excluded: chain B residue 567 THR 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 H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 163 optimal weight: 0.0870 chunk 105 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 27 optimal weight: 0.0040 chunk 26 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 179 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 overall best weight: 0.0906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 425 ASN 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 = 0.4037 r_free = 0.4037 target = 0.171572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134006 restraints weight = 20239.544| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.92 r_work: 0.3255 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17435 Z= 0.095 Angle : 0.441 6.261 23519 Z= 0.238 Chirality : 0.035 0.212 2558 Planarity : 0.004 0.064 3009 Dihedral : 3.871 22.696 2310 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.41 % Allowed : 12.98 % Favored : 85.61 % 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: 0.70 (0.19), residues: 2072 helix: 1.21 (0.14), residues: 1509 sheet: -1.93 (0.77), residues: 42 loop : -1.46 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.004 0.000 HIS A 279 PHE 0.014 0.001 PHE B 445 TYR 0.024 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 1076) hydrogen bonds : angle 3.97235 ( 3186) metal coordination : bond 0.00663 ( 4) metal coordination : angle 4.47467 ( 2) covalent geometry : bond 0.00188 (17431) covalent geometry : angle 0.43943 (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 229 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6414 (tpp) cc_final: 0.6004 (mmt) REVERT: A 160 PHE cc_start: 0.8079 (m-80) cc_final: 0.7696 (m-80) REVERT: A 425 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8058 (t0) REVERT: A 450 GLU cc_start: 0.7966 (tp30) cc_final: 0.7684 (tp30) REVERT: A 565 GLN cc_start: 0.5908 (mp10) cc_final: 0.5591 (mm110) REVERT: E 55 GLU cc_start: 0.6990 (pm20) cc_final: 0.6623 (pm20) REVERT: E 270 MET cc_start: 0.5742 (tpp) cc_final: 0.5025 (tpp) REVERT: C 55 LYS cc_start: 0.7558 (pttt) cc_final: 0.7091 (pttm) REVERT: B 152 LEU cc_start: 0.7459 (mt) cc_final: 0.7229 (mt) REVERT: B 246 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8142 (t) REVERT: B 392 ASP cc_start: 0.7046 (t0) cc_final: 0.6817 (t0) REVERT: B 446 LYS cc_start: 0.8438 (tptm) cc_final: 0.8043 (tptt) REVERT: G 6 MET cc_start: 0.8687 (ttp) cc_final: 0.8394 (ttt) REVERT: H 59 GLU cc_start: 0.7869 (pp20) cc_final: 0.7009 (pp20) REVERT: I 195 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8184 (mtpp) REVERT: I 222 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6689 (tm-30) outliers start: 26 outliers final: 17 residues processed: 218 average time/residue: 0.2859 time to fit residues: 95.8232 Evaluate side-chains 211 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 373 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 245 ASP 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 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 526 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** 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 = 0.4012 r_free = 0.4012 target = 0.169136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131047 restraints weight = 20498.602| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.93 r_work: 0.3349 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17435 Z= 0.134 Angle : 0.487 13.857 23519 Z= 0.256 Chirality : 0.037 0.263 2558 Planarity : 0.004 0.058 3009 Dihedral : 3.882 22.491 2310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 13.74 % Favored : 85.13 % 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: 0.59 (0.19), residues: 2072 helix: 1.13 (0.14), residues: 1508 sheet: -1.93 (0.78), residues: 42 loop : -1.49 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.005 0.001 HIS E 88 PHE 0.022 0.001 PHE C 79 TYR 0.029 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1076) hydrogen bonds : angle 4.02750 ( 3186) metal coordination : bond 0.00878 ( 4) metal coordination : angle 4.49016 ( 2) covalent geometry : bond 0.00310 (17431) covalent geometry : angle 0.48547 (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 217 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6532 (tpp) cc_final: 0.6090 (mmt) REVERT: A 160 PHE cc_start: 0.8207 (m-80) cc_final: 0.7826 (m-80) REVERT: A 445 PHE cc_start: 0.7960 (m-10) cc_final: 0.7090 (m-10) REVERT: A 450 GLU cc_start: 0.7990 (tp30) cc_final: 0.7726 (tp30) REVERT: A 565 GLN cc_start: 0.5963 (mp10) cc_final: 0.5618 (mm110) REVERT: E 270 MET cc_start: 0.5806 (tpp) cc_final: 0.5102 (tpp) REVERT: C 55 LYS cc_start: 0.7609 (pttt) cc_final: 0.7166 (pttm) REVERT: B 152 LEU cc_start: 0.7484 (mt) cc_final: 0.7251 (mt) REVERT: B 446 LYS cc_start: 0.8461 (tptm) cc_final: 0.8088 (tptt) REVERT: G 6 MET cc_start: 0.8809 (ttp) cc_final: 0.8505 (ttt) REVERT: H 59 GLU cc_start: 0.7995 (pp20) cc_final: 0.7643 (pp20) REVERT: H 111 ASP cc_start: 0.8354 (t0) cc_final: 0.7967 (t0) REVERT: I 195 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8246 (mtpp) REVERT: I 222 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6694 (tm-30) outliers start: 21 outliers final: 17 residues processed: 208 average time/residue: 0.2885 time to fit residues: 91.6972 Evaluate side-chains 204 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain E residue 245 ASP 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 258 VAL Chi-restraints excluded: chain B residue 526 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 100 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 171 optimal weight: 0.0020 chunk 154 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 overall best weight: 0.2866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** 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 = 0.4017 r_free = 0.4017 target = 0.169722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131752 restraints weight = 20411.288| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.93 r_work: 0.3379 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17435 Z= 0.108 Angle : 0.472 13.933 23519 Z= 0.249 Chirality : 0.036 0.199 2558 Planarity : 0.003 0.053 3009 Dihedral : 3.857 22.365 2310 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.03 % Allowed : 14.39 % 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: 0.75 (0.19), residues: 2072 helix: 1.24 (0.14), residues: 1508 sheet: -1.85 (0.79), residues: 42 loop : -1.42 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.000 HIS E 88 PHE 0.013 0.001 PHE C 79 TYR 0.025 0.001 TYR E 253 ARG 0.010 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 1076) hydrogen bonds : angle 3.97063 ( 3186) metal coordination : bond 0.00809 ( 4) metal coordination : angle 4.27650 ( 2) covalent geometry : bond 0.00236 (17431) covalent geometry : angle 0.47077 (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 222 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6550 (tpp) cc_final: 0.6124 (mmt) REVERT: A 160 PHE cc_start: 0.8213 (m-80) cc_final: 0.7855 (m-80) REVERT: A 450 GLU cc_start: 0.7966 (tp30) cc_final: 0.7706 (tp30) REVERT: A 565 GLN cc_start: 0.5912 (mp10) cc_final: 0.5664 (mm110) REVERT: E 55 GLU cc_start: 0.7026 (pm20) cc_final: 0.6618 (pm20) REVERT: E 186 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7618 (t0) REVERT: E 270 MET cc_start: 0.5842 (tpp) cc_final: 0.5113 (tpp) REVERT: C 55 LYS cc_start: 0.7529 (pttt) cc_final: 0.7114 (pttm) REVERT: B 152 LEU cc_start: 0.7486 (mt) cc_final: 0.7258 (mt) REVERT: B 446 LYS cc_start: 0.8451 (tptm) cc_final: 0.8084 (tptt) REVERT: G 6 MET cc_start: 0.8761 (ttp) cc_final: 0.8549 (ttt) REVERT: H 59 GLU cc_start: 0.7968 (pp20) cc_final: 0.7123 (pp20) REVERT: H 111 ASP cc_start: 0.8294 (t0) cc_final: 0.7941 (t0) REVERT: I 195 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8236 (mtpp) REVERT: I 222 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6674 (tm-30) outliers start: 19 outliers final: 17 residues processed: 213 average time/residue: 0.2873 time to fit residues: 93.0335 Evaluate side-chains 214 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 373 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 245 ASP 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 258 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 526 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 0.0980 chunk 180 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 chunk 141 optimal weight: 0.0970 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131985 restraints weight = 20414.524| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3377 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 17435 Z= 0.151 Angle : 0.722 59.193 23519 Z= 0.421 Chirality : 0.036 0.201 2558 Planarity : 0.004 0.052 3009 Dihedral : 3.878 22.395 2310 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.03 % Allowed : 14.44 % Favored : 84.53 % Cbeta Deviations : 0.05 % 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: 0.74 (0.19), residues: 2072 helix: 1.24 (0.14), residues: 1504 sheet: -1.89 (0.78), residues: 42 loop : -1.44 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.000 HIS E 88 PHE 0.014 0.001 PHE C 79 TYR 0.023 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 1076) hydrogen bonds : angle 3.97763 ( 3186) metal coordination : bond 0.00805 ( 4) metal coordination : angle 4.27812 ( 2) covalent geometry : bond 0.00318 (17431) covalent geometry : angle 0.72104 (23517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10002.82 seconds wall clock time: 174 minutes 21.54 seconds (10461.54 seconds total)