Starting phenix.real_space_refine on Mon Mar 18 01:02:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_36134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_36134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_36134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_36134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/03_2024/8jau_36134.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.75, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 6.11 Conformation dependent library (CDL) restraints added in 3.0 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: 1.52 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: 4.98 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5569 1.34 - 1.46: 3486 1.46 - 1.58: 8237 1.58 - 1.69: 0 1.69 - 1.81: 139 Bond restraints: 17431 Sorted by residual: bond pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" N MET I 26 " pdb=" CA MET I 26 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 290 " pdb=" CG2 THR A 290 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB THR B 290 " pdb=" CG2 THR B 290 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 17426 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 333 106.31 - 113.23: 9433 113.23 - 120.16: 6385 120.16 - 127.08: 7203 127.08 - 134.01: 163 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 2.440 nonbonded pdb=" OG1 THR C 23 " pdb=" OE1 GLU C 26 " model vdw 2.245 2.440 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN B 434 " model vdw 2.282 2.520 nonbonded pdb=" ND2 ASN B 482 " pdb=" O GLY B 519 " model vdw 2.282 2.520 nonbonded pdb=" NH1 ARG B 103 " pdb=" OH TYR B 107 " model vdw 2.289 2.520 ... (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 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: 11.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 26.460 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.880 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.480 ------------------------------------------------------------------------------- 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 17431 Z= 0.255 Angle : 0.520 6.830 23517 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 1.687 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: 0.3142 time to fit residues: 127.1994 Evaluate side-chains 194 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 0.0020 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 119 optimal weight: 0.0980 chunk 186 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 82 GLN I 116 ASN I 156 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17431 Z= 0.172 Angle : 0.476 6.290 23517 Z= 0.260 Chirality : 0.036 0.142 2558 Planarity : 0.004 0.051 3009 Dihedral : 4.035 19.398 2310 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.49 % Allowed : 5.35 % Favored : 94.16 % 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: -0.11 (0.18), residues: 2072 helix: 0.57 (0.13), residues: 1502 sheet: -2.27 (0.73), residues: 40 loop : -1.58 (0.25), residues: 530 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 E 64 TYR 0.016 0.001 TYR E 253 ARG 0.005 0.000 ARG I 251 *********************** 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 221 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6581 (tpp) cc_final: 0.6310 (mmt) REVERT: B 392 ASP cc_start: 0.6850 (t0) cc_final: 0.6580 (t0) REVERT: B 445 PHE cc_start: 0.7780 (m-10) cc_final: 0.7543 (m-10) REVERT: B 451 MET cc_start: 0.7189 (mmt) cc_final: 0.6976 (mmt) outliers start: 9 outliers final: 5 residues processed: 216 average time/residue: 0.2994 time to fit residues: 98.5687 Evaluate side-chains 198 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 306 GLN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17431 Z= 0.246 Angle : 0.478 5.748 23517 Z= 0.257 Chirality : 0.037 0.178 2558 Planarity : 0.004 0.052 3009 Dihedral : 3.999 19.174 2310 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.19 % Allowed : 8.65 % Favored : 90.16 % 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: 0.10 (0.18), residues: 2072 helix: 0.76 (0.13), residues: 1495 sheet: -2.18 (0.73), residues: 40 loop : -1.58 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 35 HIS 0.004 0.001 HIS A 452 PHE 0.014 0.001 PHE E 64 TYR 0.020 0.001 TYR E 253 ARG 0.006 0.000 ARG I 251 *********************** 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 224 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 2.052 Fit side-chains REVERT: A 156 MET cc_start: 0.6627 (tpp) cc_final: 0.6225 (mmt) REVERT: A 160 PHE cc_start: 0.8131 (m-80) cc_final: 0.7855 (m-80) REVERT: A 303 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 445 PHE cc_start: 0.7968 (m-10) cc_final: 0.7187 (m-10) REVERT: E 270 MET cc_start: 0.6397 (tpp) cc_final: 0.5824 (tpp) REVERT: B 392 ASP cc_start: 0.6933 (t0) cc_final: 0.6686 (t0) REVERT: B 443 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7573 (mmt180) REVERT: B 445 PHE cc_start: 0.7666 (m-10) cc_final: 0.7420 (m-10) REVERT: B 451 MET cc_start: 0.7223 (mmt) cc_final: 0.6969 (mmt) REVERT: H 59 GLU cc_start: 0.7931 (pp20) cc_final: 0.7252 (pp20) REVERT: H 63 ARG cc_start: 0.7722 (ptm-80) cc_final: 0.7492 (ptm160) outliers start: 22 outliers final: 16 residues processed: 215 average time/residue: 0.3201 time to fit residues: 104.8509 Evaluate side-chains 204 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 303 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 411 LEU 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 184 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS G 49 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17431 Z= 0.233 Angle : 0.464 5.652 23517 Z= 0.249 Chirality : 0.036 0.178 2558 Planarity : 0.003 0.051 3009 Dihedral : 3.972 19.087 2310 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.41 % Allowed : 9.84 % Favored : 88.75 % 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: 0.20 (0.18), residues: 2072 helix: 0.84 (0.14), residues: 1504 sheet: -2.32 (0.72), residues: 40 loop : -1.58 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 35 HIS 0.003 0.001 HIS A 452 PHE 0.013 0.001 PHE E 64 TYR 0.016 0.001 TYR A 488 ARG 0.005 0.000 ARG I 251 *********************** 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 222 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6593 (tpp) cc_final: 0.6182 (mmt) REVERT: A 160 PHE cc_start: 0.8134 (m-80) cc_final: 0.7874 (m-80) REVERT: A 445 PHE cc_start: 0.7978 (m-10) cc_final: 0.7171 (m-10) REVERT: B 392 ASP cc_start: 0.6907 (t0) cc_final: 0.6685 (t0) REVERT: B 443 ARG cc_start: 0.7775 (mmt180) cc_final: 0.7550 (mmt180) REVERT: B 451 MET cc_start: 0.7217 (mmt) cc_final: 0.6975 (mmt) REVERT: H 59 GLU cc_start: 0.7939 (pp20) cc_final: 0.7275 (pp20) outliers start: 26 outliers final: 20 residues processed: 210 average time/residue: 0.2937 time to fit residues: 92.7079 Evaluate side-chains 205 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 66 THR 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 165 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS H 108 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17431 Z= 0.292 Angle : 0.493 6.917 23517 Z= 0.263 Chirality : 0.038 0.183 2558 Planarity : 0.004 0.051 3009 Dihedral : 4.024 19.070 2310 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.06 % Allowed : 10.44 % Favored : 87.51 % 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: 0.14 (0.18), residues: 2072 helix: 0.78 (0.13), residues: 1510 sheet: -2.35 (0.72), residues: 40 loop : -1.57 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 35 HIS 0.003 0.001 HIS E 88 PHE 0.014 0.001 PHE B 101 TYR 0.017 0.001 TYR A 294 ARG 0.006 0.000 ARG I 251 *********************** 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 236 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 1.967 Fit side-chains REVERT: A 156 MET cc_start: 0.6581 (tpp) cc_final: 0.6147 (mmt) REVERT: A 160 PHE cc_start: 0.8129 (m-80) cc_final: 0.7850 (m-80) REVERT: A 445 PHE cc_start: 0.7926 (m-10) cc_final: 0.7087 (m-10) REVERT: E 270 MET cc_start: 0.6247 (tpp) cc_final: 0.5636 (tpp) REVERT: C 43 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7512 (mtm110) REVERT: B 392 ASP cc_start: 0.6948 (t0) cc_final: 0.6746 (t0) REVERT: B 446 LYS cc_start: 0.8385 (tptm) cc_final: 0.8176 (tptt) REVERT: B 451 MET cc_start: 0.7180 (mmt) cc_final: 0.6903 (mmt) REVERT: H 59 GLU cc_start: 0.7973 (pp20) cc_final: 0.7703 (pp20) outliers start: 38 outliers final: 30 residues processed: 222 average time/residue: 0.2871 time to fit residues: 97.2737 Evaluate side-chains 216 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 151 THR 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 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER 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 411 LEU Chi-restraints excluded: chain B residue 526 SER 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 G residue 66 THR 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 Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 198 optimal weight: 0.0770 chunk 164 optimal weight: 0.0470 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17431 Z= 0.177 Angle : 0.451 5.638 23517 Z= 0.242 Chirality : 0.035 0.180 2558 Planarity : 0.003 0.049 3009 Dihedral : 3.941 18.864 2310 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 11.57 % Favored : 86.80 % 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: 0.32 (0.19), residues: 2072 helix: 0.95 (0.14), residues: 1517 sheet: -2.31 (0.72), residues: 40 loop : -1.66 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 14 HIS 0.004 0.001 HIS A 279 PHE 0.021 0.001 PHE B 445 TYR 0.025 0.001 TYR I 49 ARG 0.007 0.000 ARG I 251 *********************** 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 228 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.815 Fit side-chains REVERT: A 156 MET cc_start: 0.6631 (tpp) cc_final: 0.6211 (mmt) REVERT: A 160 PHE cc_start: 0.8127 (m-80) cc_final: 0.7846 (m-80) REVERT: A 445 PHE cc_start: 0.7882 (m-10) cc_final: 0.7131 (m-10) REVERT: E 270 MET cc_start: 0.6303 (tpp) cc_final: 0.5691 (tpp) REVERT: C 43 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7376 (mtm180) REVERT: C 50 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7390 (tp) REVERT: B 246 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8665 (t) REVERT: B 446 LYS cc_start: 0.8357 (tptm) cc_final: 0.8145 (tptt) REVERT: B 451 MET cc_start: 0.7155 (mmt) cc_final: 0.6898 (mmt) REVERT: G 6 MET cc_start: 0.8600 (ttp) cc_final: 0.8246 (ttt) REVERT: H 59 GLU cc_start: 0.7939 (pp20) cc_final: 0.7674 (pp20) outliers start: 30 outliers final: 23 residues processed: 214 average time/residue: 0.2891 time to fit residues: 95.0790 Evaluate side-chains 209 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.865 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 50 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 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 411 LEU 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 G residue 66 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS I 82 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17431 Z= 0.268 Angle : 0.485 7.153 23517 Z= 0.258 Chirality : 0.037 0.189 2558 Planarity : 0.004 0.057 3009 Dihedral : 3.992 21.130 2310 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 2.11 % Allowed : 12.44 % Favored : 85.45 % 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: 0.30 (0.19), residues: 2072 helix: 0.93 (0.14), residues: 1503 sheet: -2.37 (0.73), residues: 40 loop : -1.61 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 147 HIS 0.004 0.001 HIS A 279 PHE 0.017 0.001 PHE B 445 TYR 0.029 0.001 TYR I 49 ARG 0.007 0.000 ARG I 251 *********************** 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 234 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6557 (tpp) cc_final: 0.6148 (mmt) REVERT: A 160 PHE cc_start: 0.8143 (m-80) cc_final: 0.7865 (m-80) REVERT: E 270 MET cc_start: 0.6409 (tpp) cc_final: 0.6093 (tpp) REVERT: C 43 ARG cc_start: 0.7799 (ptp-170) cc_final: 0.7341 (mtm180) REVERT: C 50 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7489 (tp) REVERT: B 446 LYS cc_start: 0.8372 (tptm) cc_final: 0.8146 (tptt) REVERT: B 451 MET cc_start: 0.7174 (mmt) cc_final: 0.6911 (mmt) REVERT: G 6 MET cc_start: 0.8621 (ttp) cc_final: 0.8383 (ttt) REVERT: G 51 LEU cc_start: 0.7674 (tp) cc_final: 0.7473 (mt) REVERT: H 59 GLU cc_start: 0.7988 (pp20) cc_final: 0.7746 (pp20) outliers start: 39 outliers final: 30 residues processed: 218 average time/residue: 0.2860 time to fit residues: 95.2986 Evaluate side-chains 217 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN 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 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 229 CYS 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 411 LEU 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 G residue 66 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 CYS 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 122 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17431 Z= 0.193 Angle : 0.466 9.606 23517 Z= 0.248 Chirality : 0.036 0.185 2558 Planarity : 0.004 0.050 3009 Dihedral : 3.944 21.733 2310 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.73 % Allowed : 12.82 % Favored : 85.45 % 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: 0.43 (0.19), residues: 2072 helix: 1.04 (0.14), residues: 1508 sheet: -2.34 (0.73), residues: 40 loop : -1.64 (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 0.020 0.001 PHE B 445 TYR 0.028 0.001 TYR A 488 ARG 0.008 0.000 ARG I 251 *********************** 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 225 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8030 (m-30) cc_final: 0.7809 (m-30) REVERT: A 156 MET cc_start: 0.6681 (tpp) cc_final: 0.6251 (mmt) REVERT: A 160 PHE cc_start: 0.8112 (m-80) cc_final: 0.7851 (m-80) REVERT: A 445 PHE cc_start: 0.7853 (m-10) cc_final: 0.7153 (m-10) REVERT: E 270 MET cc_start: 0.6408 (tpp) cc_final: 0.6095 (tpp) REVERT: C 43 ARG cc_start: 0.7795 (ptp-170) cc_final: 0.7328 (mtm180) REVERT: C 50 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7398 (tp) REVERT: B 246 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8680 (t) REVERT: B 446 LYS cc_start: 0.8350 (tptm) cc_final: 0.8123 (tptt) REVERT: B 451 MET cc_start: 0.7176 (mmt) cc_final: 0.6941 (mmt) REVERT: G 6 MET cc_start: 0.8606 (ttp) cc_final: 0.8390 (ttt) REVERT: H 59 GLU cc_start: 0.7982 (pp20) cc_final: 0.7755 (pp20) outliers start: 32 outliers final: 28 residues processed: 212 average time/residue: 0.2803 time to fit residues: 91.5651 Evaluate side-chains 217 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain B residue 229 CYS 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 411 LEU 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 G residue 66 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** E 88 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17431 Z= 0.251 Angle : 0.495 12.991 23517 Z= 0.260 Chirality : 0.037 0.193 2558 Planarity : 0.004 0.053 3009 Dihedral : 3.962 22.592 2310 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.95 % Allowed : 12.82 % Favored : 85.24 % 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: 0.36 (0.19), residues: 2072 helix: 0.99 (0.14), residues: 1507 sheet: -2.48 (0.73), residues: 40 loop : -1.64 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 147 HIS 0.004 0.001 HIS A 279 PHE 0.014 0.001 PHE B 445 TYR 0.025 0.001 TYR A 488 ARG 0.008 0.000 ARG I 251 *********************** 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 228 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8051 (m-30) cc_final: 0.7831 (m-30) REVERT: A 156 MET cc_start: 0.6546 (tpp) cc_final: 0.6128 (mmt) REVERT: A 160 PHE cc_start: 0.8116 (m-80) cc_final: 0.7861 (m-80) REVERT: E 270 MET cc_start: 0.6358 (tpp) cc_final: 0.6060 (tpp) REVERT: C 43 ARG cc_start: 0.7803 (ptp-170) cc_final: 0.7321 (mtm180) REVERT: C 50 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7466 (tp) REVERT: B 446 LYS cc_start: 0.8330 (tptm) cc_final: 0.8091 (tptt) REVERT: B 451 MET cc_start: 0.7186 (mmt) cc_final: 0.6932 (mmt) outliers start: 36 outliers final: 33 residues processed: 213 average time/residue: 0.2905 time to fit residues: 95.2135 Evaluate side-chains 221 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 229 CYS 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 411 LEU 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 G residue 66 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 0.3980 chunk 204 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 129 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17431 Z= 0.233 Angle : 0.491 12.539 23517 Z= 0.258 Chirality : 0.037 0.195 2558 Planarity : 0.004 0.052 3009 Dihedral : 3.960 18.895 2310 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.84 % Allowed : 13.09 % Favored : 85.07 % 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: 0.38 (0.19), residues: 2072 helix: 1.01 (0.14), residues: 1502 sheet: -2.42 (0.73), residues: 40 loop : -1.63 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 35 HIS 0.004 0.001 HIS A 452 PHE 0.023 0.001 PHE B 445 TYR 0.029 0.001 TYR A 488 ARG 0.008 0.000 ARG I 251 ********************** 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 227 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8045 (m-30) cc_final: 0.7827 (m-30) REVERT: A 156 MET cc_start: 0.6551 (tpp) cc_final: 0.6134 (mmt) REVERT: A 160 PHE cc_start: 0.8109 (m-80) cc_final: 0.7876 (m-80) REVERT: E 270 MET cc_start: 0.6400 (tpp) cc_final: 0.6127 (tpp) REVERT: C 43 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7300 (mtm180) REVERT: C 50 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 446 LYS cc_start: 0.8342 (tptm) cc_final: 0.8102 (tptt) REVERT: B 451 MET cc_start: 0.7171 (mmt) cc_final: 0.6922 (mmt) REVERT: H 59 GLU cc_start: 0.8060 (pp20) cc_final: 0.7446 (pp20) REVERT: I 236 MET cc_start: 0.6537 (tmm) cc_final: 0.5797 (tmm) outliers start: 34 outliers final: 32 residues processed: 213 average time/residue: 0.2569 time to fit residues: 83.4955 Evaluate side-chains 219 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 229 CYS 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 411 LEU 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 G residue 66 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3987 r_free = 0.3987 target = 0.166668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127334 restraints weight = 20472.126| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.99 r_work: 0.3288 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17431 Z= 0.258 Angle : 0.505 12.395 23517 Z= 0.265 Chirality : 0.037 0.198 2558 Planarity : 0.004 0.052 3009 Dihedral : 3.994 19.088 2310 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.78 % Allowed : 13.36 % Favored : 84.86 % 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: 0.36 (0.19), residues: 2072 helix: 0.99 (0.14), residues: 1508 sheet: -2.48 (0.73), residues: 40 loop : -1.64 (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 E 88 PHE 0.019 0.001 PHE B 445 TYR 0.035 0.001 TYR E 253 ARG 0.008 0.000 ARG I 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4047.97 seconds wall clock time: 75 minutes 26.14 seconds (4526.14 seconds total)