Starting phenix.real_space_refine on Sun Mar 17 14:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/03_2024/8sh2_40477.pdb" } resolution = 3.74 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 11483 2.51 5 N 3122 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 18038 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3030 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "H" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "I" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 749 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "K" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 725 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain breaks: 1 Chain: "L" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Chain: "C" Number of atoms: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3066 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 361} Chain breaks: 1 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3080 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain: "D" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3086 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 364} Time building chain proxies: 9.44, per 1000 atoms: 0.52 Number of scatterers: 18038 At special positions: 0 Unit cell: (139.44, 141.93, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 3324 8.00 N 3122 7.00 C 11483 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: 6.94 Conformation dependent library (CDL) restraints added in 3.4 seconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 41 sheets defined 16.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.825A pdb=" N ALA B 348 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.584A pdb=" N VAL B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 removed outlier: 3.566A pdb=" N VAL B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.073A pdb=" N PHE B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 36 Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.891A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.696A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 83 Processing helix chain 'H' and resid 99 through 109 Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.557A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 37 removed outlier: 3.550A pdb=" N LEU J 37 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.720A pdb=" N LEU J 70 " --> pdb=" O PRO J 66 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS J 72 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 Processing helix chain 'K' and resid 23 through 36 removed outlier: 3.777A pdb=" N LEU K 27 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'L' and resid 33 through 39 removed outlier: 4.060A pdb=" N SER L 39 " --> pdb=" O HIS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 removed outlier: 4.221A pdb=" N LEU L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 82 Processing helix chain 'L' and resid 96 through 111 removed outlier: 4.230A pdb=" N MET L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.760A pdb=" N CYS C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.606A pdb=" N PHE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 363 through 375 removed outlier: 3.934A pdb=" N PHE D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 385 Processing helix chain 'D' and resid 387 through 397 removed outlier: 3.800A pdb=" N ARG D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.900A pdb=" N GLU B 84 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG B 134 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLN B 131 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP B 122 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 211 through 212 removed outlier: 7.175A pdb=" N THR B 211 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU B 257 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU B 254 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 222 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.905A pdb=" N SER B 272 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 284 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B 280 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR B 300 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 282 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP B 298 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 284 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 296 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 286 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 8 removed outlier: 7.033A pdb=" N THR E 13 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N LYS F 32 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N PHE E 15 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 43 through 45 removed outlier: 3.664A pdb=" N LEU G 77 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR G 13 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LYS H 32 " --> pdb=" O THR G 13 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N PHE G 15 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.727A pdb=" N VAL I 75 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 77 " --> pdb=" O ARG I 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 13 through 19 removed outlier: 8.887A pdb=" N VAL K 75 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET K 6 " --> pdb=" O VAL K 75 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU K 77 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG K 8 " --> pdb=" O LEU K 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 28 through 32 Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.648A pdb=" N VAL C 46 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.974A pdb=" N GLU C 84 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG C 134 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLN C 131 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 122 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 118 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 146 removed outlier: 3.709A pdb=" N GLY C 162 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AC2, first strand: chain 'C' and resid 211 through 212 removed outlier: 6.873A pdb=" N THR C 211 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU C 257 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP C 244 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 272 through 275 removed outlier: 4.222A pdb=" N SER C 272 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 284 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS C 280 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR C 300 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE C 282 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP C 298 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE C 284 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP C 296 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 286 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 297 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 322 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.503A pdb=" N VAL A 36 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 77 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AC7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.872A pdb=" N GLU A 84 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG A 134 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 131 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP A 122 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 118 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AC9, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.880A pdb=" N LYS A 156 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 198 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 158 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS A 196 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 160 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS A 194 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 162 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 149 through 153 removed outlier: 4.880A pdb=" N LYS A 156 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 198 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 158 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS A 196 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 160 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS A 194 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 162 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 211 through 212 removed outlier: 7.013A pdb=" N THR A 211 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLU A 257 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 254 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 261 through 262 removed outlier: 7.731A pdb=" N GLN A 261 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLN A 309 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 294 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 287 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP A 296 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 282 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHE A 284 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 273 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 323 through 326 Processing sheet with id=AD5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD6, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AD7, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.927A pdb=" N GLU D 84 " --> pdb=" O TRP D 132 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ARG D 134 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN D 131 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP D 122 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE D 118 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD9, first strand: chain 'D' and resid 149 through 153 Processing sheet with id=AE1, first strand: chain 'D' and resid 175 through 177 Processing sheet with id=AE2, first strand: chain 'D' and resid 211 through 212 removed outlier: 7.282A pdb=" N THR D 211 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLU D 257 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 254 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 245 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET D 242 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 236 " --> pdb=" O MET D 242 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP D 244 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.173A pdb=" N LEU D 273 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE D 284 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE D 282 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 285 " --> pdb=" O ASP D 296 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP D 296 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE D 287 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 294 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 323 through 326 Processing sheet with id=AE5, first strand: chain 'D' and resid 337 through 338 594 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 7.40 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: 5645 1.34 - 1.46: 4495 1.46 - 1.58: 8241 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 18540 Sorted by residual: bond pdb=" C SER A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.01e-02 9.80e+03 1.47e+01 bond pdb=" C HIS C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.331 1.360 -0.029 7.90e-03 1.60e+04 1.31e+01 bond pdb=" N LEU I 35 " pdb=" CA LEU I 35 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.66e+00 bond pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.31e-02 5.83e+03 8.45e+00 bond pdb=" C SER A 181 " pdb=" N PHE A 182 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.27e+00 ... (remaining 18535 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.23: 421 105.23 - 112.62: 9108 112.62 - 120.01: 6943 120.01 - 127.39: 8362 127.39 - 134.78: 310 Bond angle restraints: 25144 Sorted by residual: angle pdb=" N PHE B 233 " pdb=" CA PHE B 233 " pdb=" C PHE B 233 " ideal model delta sigma weight residual 107.49 118.88 -11.39 1.74e+00 3.30e-01 4.29e+01 angle pdb=" N VAL B 276 " pdb=" CA VAL B 276 " pdb=" C VAL B 276 " ideal model delta sigma weight residual 111.45 105.54 5.91 9.30e-01 1.16e+00 4.04e+01 angle pdb=" C LYS E 46 " pdb=" N ASP E 47 " pdb=" CA ASP E 47 " ideal model delta sigma weight residual 122.82 131.45 -8.63 1.42e+00 4.96e-01 3.69e+01 angle pdb=" N GLY B 161 " pdb=" CA GLY B 161 " pdb=" C GLY B 161 " ideal model delta sigma weight residual 111.80 121.89 -10.09 1.82e+00 3.02e-01 3.07e+01 angle pdb=" C LYS B 154 " pdb=" CA LYS B 154 " pdb=" CB LYS B 154 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.02e+01 ... (remaining 25139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9906 17.75 - 35.50: 830 35.50 - 53.25: 120 53.25 - 71.00: 23 71.00 - 88.75: 8 Dihedral angle restraints: 10887 sinusoidal: 4391 harmonic: 6496 Sorted by residual: dihedral pdb=" CA LEU B 320 " pdb=" C LEU B 320 " pdb=" N TRP B 321 " pdb=" CA TRP B 321 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA HIS C 43 " pdb=" C HIS C 43 " pdb=" N MET C 44 " pdb=" CA MET C 44 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" N ARG B 65 " pdb=" CA ARG B 65 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 10884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2412 0.101 - 0.201: 228 0.201 - 0.302: 21 0.302 - 0.402: 4 0.402 - 0.503: 4 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CB ILE C 158 " pdb=" CA ILE C 158 " pdb=" CG1 ILE C 158 " pdb=" CG2 ILE C 158 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE J 65 " pdb=" CA ILE J 65 " pdb=" CG1 ILE J 65 " pdb=" CG2 ILE J 65 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB ILE H 30 " pdb=" CA ILE H 30 " pdb=" CG1 ILE H 30 " pdb=" CG2 ILE H 30 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 2666 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 383 " 0.028 2.00e-02 2.50e+03 3.21e-02 2.58e+01 pdb=" CG TRP D 383 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP D 383 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP D 383 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 383 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP D 383 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 383 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 383 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 383 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 383 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.036 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE H 29 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 65 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO F 66 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " -0.046 5.00e-02 4.00e+02 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5827 2.84 - 3.35: 15674 3.35 - 3.87: 33158 3.87 - 4.38: 37076 4.38 - 4.90: 60601 Nonbonded interactions: 152336 Sorted by model distance: nonbonded pdb=" O LYS H 80 " pdb=" OG1 THR H 84 " model vdw 2.321 2.440 nonbonded pdb=" O LYS J 80 " pdb=" OG1 THR J 84 " model vdw 2.329 2.440 nonbonded pdb=" O ARG G 9 " pdb=" OG1 THR G 12 " model vdw 2.353 2.440 nonbonded pdb=" OG1 THR C 288 " pdb=" OD1 ASP C 290 " model vdw 2.355 2.440 nonbonded pdb=" OG SER C 358 " pdb=" O GLN C 360 " model vdw 2.355 2.440 ... (remaining 152331 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' and (resid 25 through 381 or resid 387 through 406)) selection = chain 'B' selection = (chain 'C' and (resid 25 through 381 or resid 387 through 406)) selection = (chain 'D' and (resid 25 through 381 or resid 387 through 406)) } ncs_group { reference = (chain 'E' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'G' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'I' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'K' and resid 1 through 96) } ncs_group { reference = (chain 'F' and (resid 17 through 47 or resid 58 through 112)) selection = (chain 'H' and (resid 17 through 47 or resid 55 through 56 or resid 60 through 1 \ 12)) selection = chain 'J' selection = (chain 'L' and (resid 17 through 47 or resid 58 through 112)) } 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 group one per residue 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: 3.300 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: 7.600 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 47.840 Find NCS groups from input model: 1.250 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4096 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 : 0.006 0.059 18540 Z= 0.384 Angle : 1.197 14.848 25144 Z= 0.668 Chirality : 0.063 0.503 2669 Planarity : 0.008 0.084 3243 Dihedral : 13.349 88.748 6697 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.35 % Allowed : 1.72 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.82 (0.15), residues: 2214 helix: -3.16 (0.20), residues: 356 sheet: -0.91 (0.20), residues: 589 loop : -1.98 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP D 383 HIS 0.013 0.001 HIS F 68 PHE 0.063 0.003 PHE H 29 TYR 0.025 0.002 TYR B 247 ARG 0.011 0.001 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 444 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.5883 (pmm) cc_final: 0.5513 (mtm) REVERT: B 121 LEU cc_start: 0.8424 (tp) cc_final: 0.7461 (tp) REVERT: B 146 ASP cc_start: 0.5883 (p0) cc_final: 0.5560 (p0) REVERT: B 147 LYS cc_start: 0.5493 (mttt) cc_final: 0.4358 (mttt) REVERT: B 292 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9146 (tm-30) REVERT: B 373 ILE cc_start: 0.7510 (mm) cc_final: 0.7307 (mm) REVERT: E 86 GLU cc_start: 0.6458 (tm-30) cc_final: 0.5382 (mp0) REVERT: F 30 ILE cc_start: 0.6690 (tp) cc_final: 0.6242 (tp) REVERT: F 83 TYR cc_start: 0.7439 (m-80) cc_final: 0.7052 (m-80) REVERT: F 98 GLU cc_start: 0.8295 (pm20) cc_final: 0.8037 (tt0) REVERT: G 6 MET cc_start: 0.7852 (mmp) cc_final: 0.7629 (mmm) REVERT: G 82 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7052 (p0) REVERT: H 45 MET cc_start: 0.7604 (ttt) cc_final: 0.7283 (ppp) REVERT: H 58 ASN cc_start: 0.7215 (m110) cc_final: 0.6878 (m-40) REVERT: H 105 MET cc_start: 0.6465 (tpt) cc_final: 0.5669 (mmp) REVERT: J 45 MET cc_start: 0.1515 (mtt) cc_final: 0.0529 (ttt) REVERT: K 23 THR cc_start: 0.8956 (p) cc_final: 0.8589 (t) REVERT: K 25 PHE cc_start: 0.9685 (m-80) cc_final: 0.9305 (m-80) REVERT: K 91 GLU cc_start: 0.8674 (tp30) cc_final: 0.8070 (pp20) REVERT: L 29 PHE cc_start: 0.6810 (m-80) cc_final: 0.6094 (m-80) REVERT: L 105 MET cc_start: 0.4834 (ppp) cc_final: 0.4245 (ppp) REVERT: C 88 PRO cc_start: 0.7125 (Cg_endo) cc_final: 0.6629 (Cg_exo) REVERT: C 120 MET cc_start: 0.6089 (tmm) cc_final: 0.5683 (tmm) REVERT: C 369 LEU cc_start: 0.7568 (mt) cc_final: 0.7367 (mp) REVERT: C 386 LEU cc_start: 0.1724 (OUTLIER) cc_final: 0.0985 (pp) REVERT: A 61 PHE cc_start: 0.5688 (t80) cc_final: 0.5344 (t80) REVERT: A 203 PHE cc_start: 0.7579 (m-80) cc_final: 0.7318 (m-10) REVERT: A 284 PHE cc_start: 0.2844 (t80) cc_final: 0.2454 (t80) REVERT: D 65 ARG cc_start: 0.6930 (ptm160) cc_final: 0.6549 (ptm-80) REVERT: D 254 GLU cc_start: 0.8112 (tt0) cc_final: 0.7437 (tp30) REVERT: D 307 TRP cc_start: 0.5825 (m100) cc_final: 0.5253 (m100) REVERT: D 317 LYS cc_start: 0.4421 (pttm) cc_final: 0.3717 (mttt) REVERT: D 331 GLU cc_start: 0.6892 (mt-10) cc_final: 0.5974 (mt-10) REVERT: D 338 CYS cc_start: 0.3184 (t) cc_final: 0.2819 (t) outliers start: 7 outliers final: 1 residues processed: 448 average time/residue: 0.3237 time to fit residues: 211.4436 Evaluate side-chains 302 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 299 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 68 HIS J 35 HIS K 10 HIS K 49 GLN L 58 ASN ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 207 GLN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS A 43 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS D 360 GLN D 396 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4423 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 18540 Z= 0.455 Angle : 0.846 11.833 25144 Z= 0.446 Chirality : 0.050 0.220 2669 Planarity : 0.007 0.067 3243 Dihedral : 6.508 50.351 2444 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.79 % Allowed : 11.56 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.53 (0.15), residues: 2214 helix: -2.01 (0.23), residues: 360 sheet: -1.27 (0.19), residues: 606 loop : -1.78 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 321 HIS 0.014 0.002 HIS B 110 PHE 0.032 0.003 PHE F 77 TYR 0.034 0.003 TYR A 165 ARG 0.010 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 325 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.4647 (tpt) REVERT: B 121 LEU cc_start: 0.8369 (tp) cc_final: 0.7877 (tp) REVERT: B 147 LYS cc_start: 0.5598 (mttt) cc_final: 0.4961 (mttt) REVERT: B 284 PHE cc_start: 0.6184 (t80) cc_final: 0.5893 (t80) REVERT: B 292 GLN cc_start: 0.9499 (tp-100) cc_final: 0.9091 (tm-30) REVERT: F 21 LEU cc_start: 0.9143 (tp) cc_final: 0.8779 (tp) REVERT: F 72 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8232 (mttp) REVERT: F 83 TYR cc_start: 0.7692 (m-80) cc_final: 0.7051 (m-80) REVERT: F 98 GLU cc_start: 0.8433 (pm20) cc_final: 0.8116 (tt0) REVERT: G 8 ARG cc_start: 0.8764 (mtm180) cc_final: 0.8561 (mtm180) REVERT: G 82 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7138 (p0) REVERT: H 75 MET cc_start: 0.5060 (tmm) cc_final: 0.4795 (ppp) REVERT: H 83 TYR cc_start: 0.6596 (m-80) cc_final: 0.6109 (m-10) REVERT: H 105 MET cc_start: 0.6816 (tpt) cc_final: 0.5947 (mmp) REVERT: J 45 MET cc_start: 0.1179 (mtt) cc_final: 0.0179 (ttt) REVERT: K 23 THR cc_start: 0.8722 (p) cc_final: 0.8405 (t) REVERT: K 25 PHE cc_start: 0.9688 (m-80) cc_final: 0.9244 (m-80) REVERT: C 120 MET cc_start: 0.6028 (tmm) cc_final: 0.5387 (tmm) REVERT: C 121 LEU cc_start: 0.8854 (tp) cc_final: 0.8566 (tt) REVERT: C 177 PHE cc_start: 0.8219 (p90) cc_final: 0.7895 (p90) REVERT: C 233 PHE cc_start: 0.7335 (t80) cc_final: 0.6937 (t80) REVERT: A 120 MET cc_start: 0.5742 (tmm) cc_final: 0.5240 (tmm) REVERT: A 304 LYS cc_start: 0.6563 (mttp) cc_final: 0.6227 (mttp) REVERT: A 347 ARG cc_start: 0.6788 (mtt180) cc_final: 0.6280 (mtt180) REVERT: D 144 SER cc_start: 0.4018 (OUTLIER) cc_final: 0.3616 (t) REVERT: D 228 ASN cc_start: 0.7661 (p0) cc_final: 0.7435 (m-40) REVERT: D 242 MET cc_start: 0.5765 (ttp) cc_final: 0.5537 (ttp) REVERT: D 254 GLU cc_start: 0.7996 (tt0) cc_final: 0.7568 (tp30) REVERT: D 304 LYS cc_start: 0.7983 (mptt) cc_final: 0.7721 (mptt) REVERT: D 317 LYS cc_start: 0.5171 (pttm) cc_final: 0.4511 (mtpt) REVERT: D 328 ASP cc_start: 0.6616 (m-30) cc_final: 0.6414 (t0) REVERT: D 331 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6729 (mp0) outliers start: 55 outliers final: 33 residues processed: 353 average time/residue: 0.3381 time to fit residues: 172.8113 Evaluate side-chains 307 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 396 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 166 optimal weight: 0.6980 chunk 136 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN G 65 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN L 58 ASN C 292 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4331 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18540 Z= 0.191 Angle : 0.664 10.553 25144 Z= 0.335 Chirality : 0.045 0.271 2669 Planarity : 0.005 0.054 3243 Dihedral : 5.633 46.019 2444 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.84 % Allowed : 13.24 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.16), residues: 2214 helix: -1.44 (0.25), residues: 364 sheet: -1.01 (0.19), residues: 619 loop : -1.59 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 321 HIS 0.008 0.001 HIS L 27 PHE 0.039 0.002 PHE B 233 TYR 0.025 0.002 TYR A 119 ARG 0.007 0.000 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 292 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8101 (tp) cc_final: 0.7713 (tp) REVERT: B 284 PHE cc_start: 0.6251 (t80) cc_final: 0.5959 (t80) REVERT: B 292 GLN cc_start: 0.9467 (tp-100) cc_final: 0.9066 (tm-30) REVERT: E 8 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8678 (mtm-85) REVERT: F 33 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8149 (mtt90) REVERT: F 83 TYR cc_start: 0.7563 (m-80) cc_final: 0.6968 (m-80) REVERT: F 98 GLU cc_start: 0.8379 (pm20) cc_final: 0.8107 (tt0) REVERT: G 65 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9124 (pm20) REVERT: G 68 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7761 (tpp80) REVERT: G 82 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.6991 (p0) REVERT: H 45 MET cc_start: 0.8558 (ptm) cc_final: 0.8331 (ptp) REVERT: H 83 TYR cc_start: 0.6330 (m-80) cc_final: 0.5995 (m-10) REVERT: H 92 GLU cc_start: 0.8265 (pm20) cc_final: 0.7945 (tp30) REVERT: H 105 MET cc_start: 0.6705 (tpt) cc_final: 0.5791 (mmp) REVERT: J 17 MET cc_start: 0.6784 (tpp) cc_final: 0.5691 (tmm) REVERT: J 45 MET cc_start: 0.0856 (mtt) cc_final: -0.0117 (ttt) REVERT: K 23 THR cc_start: 0.8715 (p) cc_final: 0.8382 (t) REVERT: K 25 PHE cc_start: 0.9696 (m-80) cc_final: 0.9262 (m-80) REVERT: L 29 PHE cc_start: 0.6457 (m-80) cc_final: 0.5730 (m-80) REVERT: C 84 GLU cc_start: 0.8885 (pt0) cc_final: 0.8537 (pt0) REVERT: C 120 MET cc_start: 0.6082 (tmm) cc_final: 0.5534 (tmm) REVERT: C 177 PHE cc_start: 0.8234 (p90) cc_final: 0.7853 (p90) REVERT: C 370 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: C 386 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.1187 (pp) REVERT: C 396 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8086 (pm20) REVERT: A 120 MET cc_start: 0.5777 (tmm) cc_final: 0.5258 (tmm) REVERT: A 196 HIS cc_start: 0.7093 (m90) cc_final: 0.6868 (m90) REVERT: A 284 PHE cc_start: 0.3975 (t80) cc_final: 0.3035 (t80) REVERT: A 321 TRP cc_start: 0.6698 (t-100) cc_final: 0.5972 (m-10) REVERT: A 347 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6180 (mtt180) REVERT: D 254 GLU cc_start: 0.7718 (tt0) cc_final: 0.7370 (tp30) REVERT: D 304 LYS cc_start: 0.8201 (mptt) cc_final: 0.7312 (tptp) REVERT: D 317 LYS cc_start: 0.5200 (pttm) cc_final: 0.4563 (mtpt) REVERT: D 328 ASP cc_start: 0.6913 (m-30) cc_final: 0.6402 (t0) outliers start: 56 outliers final: 29 residues processed: 321 average time/residue: 0.3278 time to fit residues: 154.8994 Evaluate side-chains 300 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 TRP Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 0.0570 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN D 350 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4433 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18540 Z= 0.320 Angle : 0.705 9.574 25144 Z= 0.362 Chirality : 0.046 0.234 2669 Planarity : 0.005 0.054 3243 Dihedral : 5.799 46.498 2444 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.70 % Allowed : 14.96 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.08 (0.16), residues: 2214 helix: -1.18 (0.25), residues: 364 sheet: -1.30 (0.19), residues: 614 loop : -1.45 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 270 HIS 0.013 0.002 HIS D 271 PHE 0.035 0.002 PHE I 4 TYR 0.033 0.003 TYR D 163 ARG 0.010 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 288 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4922 (tpt) cc_final: 0.4557 (tpp) REVERT: B 121 LEU cc_start: 0.8289 (tp) cc_final: 0.7736 (tp) REVERT: B 292 GLN cc_start: 0.9505 (tp-100) cc_final: 0.9084 (tm-30) REVERT: F 72 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8586 (mtmt) REVERT: F 83 TYR cc_start: 0.7564 (m-80) cc_final: 0.7032 (m-80) REVERT: F 98 GLU cc_start: 0.8411 (pm20) cc_final: 0.8125 (tt0) REVERT: G 1 MET cc_start: 0.9079 (mpp) cc_final: 0.8173 (ptp) REVERT: G 82 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7056 (p0) REVERT: H 76 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6233 (t80) REVERT: H 105 MET cc_start: 0.6856 (tpt) cc_final: 0.6548 (tpt) REVERT: J 17 MET cc_start: 0.7145 (tpp) cc_final: 0.6334 (tmm) REVERT: J 45 MET cc_start: 0.0824 (mtt) cc_final: -0.0022 (ttt) REVERT: C 84 GLU cc_start: 0.8984 (pt0) cc_final: 0.8713 (pt0) REVERT: C 120 MET cc_start: 0.6200 (tmm) cc_final: 0.5475 (tmm) REVERT: C 177 PHE cc_start: 0.8301 (p90) cc_final: 0.7886 (p90) REVERT: C 370 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5709 (pt0) REVERT: C 396 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7997 (pm20) REVERT: A 120 MET cc_start: 0.5734 (tmm) cc_final: 0.5151 (tmm) REVERT: A 196 HIS cc_start: 0.7738 (m90) cc_final: 0.7441 (m90) REVERT: A 271 HIS cc_start: 0.7171 (p90) cc_final: 0.6925 (p90) REVERT: A 321 TRP cc_start: 0.6914 (t-100) cc_final: 0.5869 (m-10) REVERT: A 347 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6212 (mtt180) REVERT: D 144 SER cc_start: 0.3327 (OUTLIER) cc_final: 0.2962 (t) REVERT: D 254 GLU cc_start: 0.7957 (tt0) cc_final: 0.7526 (tp30) REVERT: D 304 LYS cc_start: 0.8303 (mptt) cc_final: 0.7560 (tptp) REVERT: D 317 LYS cc_start: 0.5463 (pttm) cc_final: 0.4846 (mtpt) REVERT: D 328 ASP cc_start: 0.7035 (m-30) cc_final: 0.6557 (t0) outliers start: 73 outliers final: 43 residues processed: 324 average time/residue: 0.3251 time to fit residues: 155.0230 Evaluate side-chains 309 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 262 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 181 optimal weight: 40.0000 chunk 146 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18540 Z= 0.199 Angle : 0.651 9.996 25144 Z= 0.326 Chirality : 0.044 0.251 2669 Planarity : 0.004 0.050 3243 Dihedral : 5.357 43.995 2444 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.14 % Allowed : 17.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.16), residues: 2214 helix: -0.96 (0.26), residues: 363 sheet: -1.18 (0.20), residues: 608 loop : -1.32 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 270 HIS 0.009 0.001 HIS D 271 PHE 0.035 0.001 PHE I 4 TYR 0.034 0.002 TYR L 76 ARG 0.013 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 278 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4854 (tpt) cc_final: 0.4437 (tpt) REVERT: B 121 LEU cc_start: 0.8193 (tp) cc_final: 0.7734 (tp) REVERT: B 292 GLN cc_start: 0.9480 (tp-100) cc_final: 0.9089 (tm-30) REVERT: F 83 TYR cc_start: 0.7519 (m-80) cc_final: 0.6988 (m-80) REVERT: F 98 GLU cc_start: 0.8374 (pm20) cc_final: 0.8074 (tt0) REVERT: G 1 MET cc_start: 0.9084 (mpp) cc_final: 0.8261 (ptp) REVERT: G 82 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7141 (p0) REVERT: H 76 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6367 (t80) REVERT: H 92 GLU cc_start: 0.8283 (pm20) cc_final: 0.7941 (tp30) REVERT: H 105 MET cc_start: 0.6852 (tpt) cc_final: 0.6573 (tpt) REVERT: J 45 MET cc_start: 0.0743 (mtt) cc_final: -0.0111 (ttt) REVERT: L 29 PHE cc_start: 0.6401 (m-80) cc_final: 0.5564 (m-80) REVERT: L 92 GLU cc_start: 0.7690 (tp30) cc_final: 0.7299 (tp30) REVERT: C 73 MET cc_start: 0.5978 (mpp) cc_final: 0.5758 (mpp) REVERT: C 84 GLU cc_start: 0.9024 (pt0) cc_final: 0.8736 (pt0) REVERT: C 120 MET cc_start: 0.6133 (tmm) cc_final: 0.5613 (tmm) REVERT: C 177 PHE cc_start: 0.8369 (p90) cc_final: 0.7959 (p90) REVERT: C 370 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5559 (pt0) REVERT: C 386 LEU cc_start: 0.2547 (OUTLIER) cc_final: 0.0969 (pp) REVERT: C 396 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8000 (pm20) REVERT: A 120 MET cc_start: 0.5774 (tmm) cc_final: 0.5197 (tmm) REVERT: A 196 HIS cc_start: 0.7665 (m90) cc_final: 0.7358 (m90) REVERT: A 271 HIS cc_start: 0.7018 (p90) cc_final: 0.6216 (p90) REVERT: A 284 PHE cc_start: 0.3972 (t80) cc_final: 0.3142 (t80) REVERT: A 321 TRP cc_start: 0.6612 (t-100) cc_final: 0.5809 (m-10) REVERT: A 347 ARG cc_start: 0.6666 (mtt180) cc_final: 0.6182 (mtt180) REVERT: D 31 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5258 (pm20) REVERT: D 254 GLU cc_start: 0.7844 (tt0) cc_final: 0.7412 (tp30) REVERT: D 304 LYS cc_start: 0.8322 (mptt) cc_final: 0.7593 (tptp) REVERT: D 317 LYS cc_start: 0.5434 (pttm) cc_final: 0.4707 (mtpt) REVERT: D 328 ASP cc_start: 0.7016 (m-30) cc_final: 0.6592 (t0) outliers start: 62 outliers final: 38 residues processed: 311 average time/residue: 0.3187 time to fit residues: 145.7194 Evaluate side-chains 303 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 18540 Z= 0.543 Angle : 0.872 17.951 25144 Z= 0.457 Chirality : 0.050 0.237 2669 Planarity : 0.006 0.065 3243 Dihedral : 6.411 45.787 2444 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 35.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.51 % Allowed : 18.00 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.16), residues: 2214 helix: -1.05 (0.25), residues: 374 sheet: -1.73 (0.20), residues: 605 loop : -1.50 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 270 HIS 0.017 0.002 HIS A 109 PHE 0.034 0.003 PHE D 310 TYR 0.037 0.003 TYR A 163 ARG 0.011 0.001 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 274 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.5166 (tpt) cc_final: 0.4805 (tpp) REVERT: B 121 LEU cc_start: 0.8436 (tp) cc_final: 0.7924 (tp) REVERT: B 292 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9155 (tm-30) REVERT: B 320 LEU cc_start: 0.8205 (pt) cc_final: 0.7720 (mt) REVERT: F 33 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8340 (mtt-85) REVERT: F 75 MET cc_start: 0.6330 (tpp) cc_final: 0.6124 (tpp) REVERT: F 83 TYR cc_start: 0.7547 (m-80) cc_final: 0.7103 (m-80) REVERT: F 98 GLU cc_start: 0.8558 (pm20) cc_final: 0.8024 (tt0) REVERT: G 1 MET cc_start: 0.9180 (mpp) cc_final: 0.8519 (ptp) REVERT: G 70 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6068 (pp30) REVERT: H 76 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6635 (t80) REVERT: H 92 GLU cc_start: 0.8282 (pm20) cc_final: 0.8010 (pm20) REVERT: H 105 MET cc_start: 0.7205 (tpt) cc_final: 0.6977 (tpt) REVERT: I 6 MET cc_start: 0.4221 (pmm) cc_final: 0.3112 (pmm) REVERT: J 17 MET cc_start: 0.6305 (tmm) cc_final: 0.4487 (ptt) REVERT: J 45 MET cc_start: 0.0931 (mtt) cc_final: -0.0106 (ttt) REVERT: L 45 MET cc_start: 0.5000 (ppp) cc_final: 0.3591 (pmm) REVERT: C 120 MET cc_start: 0.6488 (tmm) cc_final: 0.5776 (tmm) REVERT: C 177 PHE cc_start: 0.8385 (p90) cc_final: 0.7939 (p90) REVERT: C 370 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5674 (pt0) REVERT: C 396 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7937 (pm20) REVERT: A 120 MET cc_start: 0.5813 (tmm) cc_final: 0.5256 (tmm) REVERT: A 273 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6980 (mp) REVERT: A 304 LYS cc_start: 0.6674 (mttp) cc_final: 0.6358 (mttp) REVERT: A 328 ASP cc_start: 0.7346 (t0) cc_final: 0.7127 (t0) REVERT: A 347 ARG cc_start: 0.6742 (mtt180) cc_final: 0.6253 (mtt180) REVERT: D 78 TRP cc_start: 0.2839 (m100) cc_final: 0.2587 (m100) REVERT: D 189 ARG cc_start: 0.2891 (mtm180) cc_final: 0.2415 (mtm180) REVERT: D 304 LYS cc_start: 0.8278 (mptt) cc_final: 0.7665 (tptp) REVERT: D 328 ASP cc_start: 0.7415 (m-30) cc_final: 0.6829 (t0) outliers start: 89 outliers final: 64 residues processed: 327 average time/residue: 0.3302 time to fit residues: 157.6721 Evaluate side-chains 322 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 155 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4452 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18540 Z= 0.263 Angle : 0.716 17.482 25144 Z= 0.359 Chirality : 0.045 0.221 2669 Planarity : 0.004 0.047 3243 Dihedral : 5.716 46.398 2444 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.45 % Allowed : 19.57 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.05 (0.17), residues: 2214 helix: -0.94 (0.26), residues: 365 sheet: -1.42 (0.20), residues: 584 loop : -1.43 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 270 HIS 0.007 0.001 HIS A 271 PHE 0.033 0.002 PHE A 61 TYR 0.032 0.002 TYR L 76 ARG 0.007 0.000 ARG H 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 265 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.7301 (p90) REVERT: B 120 MET cc_start: 0.4986 (tpt) cc_final: 0.4615 (tpp) REVERT: B 121 LEU cc_start: 0.8302 (tp) cc_final: 0.7792 (tp) REVERT: B 292 GLN cc_start: 0.9547 (tp-100) cc_final: 0.9161 (tm-30) REVERT: B 320 LEU cc_start: 0.8001 (pt) cc_final: 0.7546 (mt) REVERT: F 79 TYR cc_start: 0.8432 (t80) cc_final: 0.8199 (t80) REVERT: F 83 TYR cc_start: 0.7474 (m-80) cc_final: 0.6960 (m-80) REVERT: F 98 GLU cc_start: 0.8504 (pm20) cc_final: 0.8038 (tt0) REVERT: H 58 ASN cc_start: 0.7135 (m110) cc_final: 0.6891 (m-40) REVERT: H 76 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6637 (t80) REVERT: H 92 GLU cc_start: 0.8181 (pm20) cc_final: 0.7822 (tp30) REVERT: H 105 MET cc_start: 0.7138 (tpt) cc_final: 0.6900 (tpt) REVERT: I 32 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: J 17 MET cc_start: 0.6306 (tmm) cc_final: 0.4605 (ptt) REVERT: J 45 MET cc_start: 0.0738 (mtt) cc_final: -0.0090 (ttt) REVERT: C 73 MET cc_start: 0.5908 (mpp) cc_final: 0.5453 (mpp) REVERT: C 120 MET cc_start: 0.6426 (tmm) cc_final: 0.5824 (tmm) REVERT: C 177 PHE cc_start: 0.8424 (p90) cc_final: 0.7997 (p90) REVERT: C 370 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5399 (pt0) REVERT: C 396 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8009 (pm20) REVERT: A 42 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6520 (ttp-110) REVERT: A 65 ARG cc_start: 0.6488 (ptm160) cc_final: 0.6123 (ptt180) REVERT: A 120 MET cc_start: 0.5835 (tmm) cc_final: 0.5279 (tmm) REVERT: A 347 ARG cc_start: 0.6661 (mtt180) cc_final: 0.6191 (mtt180) REVERT: D 31 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5335 (pm20) REVERT: D 120 MET cc_start: 0.5749 (tmm) cc_final: 0.5139 (tmm) REVERT: D 189 ARG cc_start: 0.2881 (mtm180) cc_final: 0.2314 (mtm180) REVERT: D 304 LYS cc_start: 0.8248 (mptt) cc_final: 0.7646 (tptp) REVERT: D 317 LYS cc_start: 0.5530 (pttm) cc_final: 0.4847 (mtpt) REVERT: D 328 ASP cc_start: 0.7290 (m-30) cc_final: 0.6797 (t0) outliers start: 68 outliers final: 51 residues processed: 306 average time/residue: 0.3225 time to fit residues: 143.2695 Evaluate side-chains 315 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 259 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.0670 chunk 84 optimal weight: 40.0000 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4479 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18540 Z= 0.307 Angle : 0.731 17.279 25144 Z= 0.370 Chirality : 0.045 0.221 2669 Planarity : 0.005 0.059 3243 Dihedral : 5.724 46.637 2444 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.11 % Allowed : 19.93 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.08 (0.17), residues: 2214 helix: -1.00 (0.26), residues: 371 sheet: -1.43 (0.20), residues: 583 loop : -1.45 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 78 HIS 0.009 0.001 HIS A 271 PHE 0.030 0.002 PHE F 77 TYR 0.036 0.002 TYR L 76 ARG 0.013 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 259 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7404 (p90) REVERT: B 120 MET cc_start: 0.5045 (tpt) cc_final: 0.4697 (tpp) REVERT: B 121 LEU cc_start: 0.8351 (tp) cc_final: 0.7857 (tp) REVERT: B 229 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6944 (mmm-85) REVERT: B 292 GLN cc_start: 0.9551 (tp-100) cc_final: 0.9157 (tm-30) REVERT: B 320 LEU cc_start: 0.7982 (pt) cc_final: 0.7537 (mt) REVERT: F 45 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8828 (pmm) REVERT: F 83 TYR cc_start: 0.7468 (m-80) cc_final: 0.7074 (m-80) REVERT: F 98 GLU cc_start: 0.8556 (pm20) cc_final: 0.8088 (tt0) REVERT: G 1 MET cc_start: 0.9111 (mpp) cc_final: 0.8554 (ptp) REVERT: H 58 ASN cc_start: 0.7136 (m110) cc_final: 0.6885 (m-40) REVERT: H 62 PHE cc_start: 0.6924 (m-10) cc_final: 0.6696 (m-10) REVERT: H 76 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6604 (t80) REVERT: H 92 GLU cc_start: 0.8150 (pm20) cc_final: 0.7791 (tp30) REVERT: J 17 MET cc_start: 0.6355 (tmm) cc_final: 0.4679 (ptt) REVERT: J 45 MET cc_start: 0.0755 (mtt) cc_final: -0.0079 (ttt) REVERT: C 73 MET cc_start: 0.5976 (mpp) cc_final: 0.5479 (mpp) REVERT: C 120 MET cc_start: 0.6447 (tmm) cc_final: 0.5853 (tmm) REVERT: C 177 PHE cc_start: 0.8410 (p90) cc_final: 0.7972 (p90) REVERT: C 370 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5205 (pt0) REVERT: C 396 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7913 (pm20) REVERT: A 42 ARG cc_start: 0.6779 (mtm-85) cc_final: 0.6512 (ttp-110) REVERT: A 65 ARG cc_start: 0.6479 (ptm160) cc_final: 0.6119 (mtm110) REVERT: A 78 TRP cc_start: 0.3078 (m100) cc_final: 0.2652 (m-10) REVERT: A 120 MET cc_start: 0.5811 (tmm) cc_final: 0.5261 (tmm) REVERT: A 196 HIS cc_start: 0.8245 (m90) cc_final: 0.7970 (m90) REVERT: A 273 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 347 ARG cc_start: 0.6689 (mtt180) cc_final: 0.6202 (mtt180) REVERT: D 120 MET cc_start: 0.5583 (tmm) cc_final: 0.5066 (tmm) REVERT: D 189 ARG cc_start: 0.2771 (mtm180) cc_final: 0.2160 (mtm180) REVERT: D 304 LYS cc_start: 0.8244 (mptt) cc_final: 0.7628 (tptp) REVERT: D 317 LYS cc_start: 0.5480 (pttm) cc_final: 0.4849 (mtpt) REVERT: D 328 ASP cc_start: 0.7241 (m-30) cc_final: 0.6823 (t0) outliers start: 81 outliers final: 63 residues processed: 307 average time/residue: 0.3356 time to fit residues: 149.7666 Evaluate side-chains 323 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 255 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 197 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 0.0470 chunk 60 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 186 optimal weight: 0.0370 chunk 196 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4368 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18540 Z= 0.177 Angle : 0.697 16.148 25144 Z= 0.343 Chirality : 0.044 0.228 2669 Planarity : 0.004 0.049 3243 Dihedral : 5.215 45.472 2444 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.79 % Allowed : 21.20 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.17), residues: 2214 helix: -0.97 (0.26), residues: 366 sheet: -1.25 (0.20), residues: 599 loop : -1.32 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 321 HIS 0.017 0.001 HIS F 68 PHE 0.040 0.002 PHE F 77 TYR 0.036 0.002 TYR L 76 ARG 0.012 0.000 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 267 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4830 (tpt) cc_final: 0.4537 (tpp) REVERT: B 121 LEU cc_start: 0.8162 (tp) cc_final: 0.7671 (tp) REVERT: B 292 GLN cc_start: 0.9521 (tp-100) cc_final: 0.9134 (tm-30) REVERT: B 320 LEU cc_start: 0.7869 (pt) cc_final: 0.7444 (mt) REVERT: E 7 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8618 (tp) REVERT: F 83 TYR cc_start: 0.7451 (m-80) cc_final: 0.7019 (m-80) REVERT: F 98 GLU cc_start: 0.8481 (pm20) cc_final: 0.8054 (tt0) REVERT: G 1 MET cc_start: 0.8992 (mpp) cc_final: 0.8376 (ptp) REVERT: H 58 ASN cc_start: 0.7119 (m110) cc_final: 0.6864 (m-40) REVERT: H 76 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6382 (t80) REVERT: H 92 GLU cc_start: 0.7953 (pm20) cc_final: 0.7603 (tp30) REVERT: J 17 MET cc_start: 0.6389 (tmm) cc_final: 0.4787 (ptt) REVERT: J 45 MET cc_start: 0.0667 (mtt) cc_final: -0.0160 (ttt) REVERT: K 1 MET cc_start: 0.3812 (tpt) cc_final: 0.3608 (tmm) REVERT: L 29 PHE cc_start: 0.6530 (m-80) cc_final: 0.5701 (m-80) REVERT: C 36 VAL cc_start: 0.6894 (OUTLIER) cc_final: 0.6526 (m) REVERT: C 73 MET cc_start: 0.5928 (mpp) cc_final: 0.5588 (mpp) REVERT: C 120 MET cc_start: 0.6347 (tmm) cc_final: 0.5736 (tmm) REVERT: C 177 PHE cc_start: 0.8448 (p90) cc_final: 0.8010 (p90) REVERT: C 370 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.4982 (pt0) REVERT: C 386 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.1255 (pp) REVERT: C 396 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8020 (pm20) REVERT: A 78 TRP cc_start: 0.2751 (m100) cc_final: 0.2238 (m-10) REVERT: A 120 MET cc_start: 0.5745 (tmm) cc_final: 0.5135 (tmm) REVERT: A 347 ARG cc_start: 0.6608 (mtt180) cc_final: 0.6114 (mtt180) REVERT: D 31 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5290 (pm20) REVERT: D 73 MET cc_start: 0.4821 (mtm) cc_final: 0.4424 (mtm) REVERT: D 78 TRP cc_start: 0.2306 (m100) cc_final: 0.1939 (m100) REVERT: D 120 MET cc_start: 0.5607 (tmm) cc_final: 0.5090 (tmm) REVERT: D 189 ARG cc_start: 0.2909 (mtm180) cc_final: 0.2368 (mtm180) REVERT: D 254 GLU cc_start: 0.7814 (tt0) cc_final: 0.7365 (tp30) REVERT: D 304 LYS cc_start: 0.8209 (mptt) cc_final: 0.7620 (tptp) REVERT: D 317 LYS cc_start: 0.5392 (pttm) cc_final: 0.4786 (mtpt) outliers start: 55 outliers final: 45 residues processed: 297 average time/residue: 0.3227 time to fit residues: 144.7552 Evaluate side-chains 293 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 242 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4426 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18540 Z= 0.226 Angle : 0.715 14.613 25144 Z= 0.356 Chirality : 0.044 0.244 2669 Planarity : 0.004 0.056 3243 Dihedral : 5.277 44.354 2444 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.94 % Allowed : 21.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.17), residues: 2214 helix: -0.96 (0.26), residues: 372 sheet: -1.14 (0.21), residues: 574 loop : -1.29 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 47 HIS 0.012 0.001 HIS F 68 PHE 0.040 0.002 PHE F 77 TYR 0.049 0.002 TYR L 76 ARG 0.018 0.000 ARG I 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 248 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4912 (tpt) cc_final: 0.4614 (tpp) REVERT: B 121 LEU cc_start: 0.8196 (tp) cc_final: 0.7694 (tp) REVERT: B 292 GLN cc_start: 0.9529 (tp-100) cc_final: 0.9162 (tm-30) REVERT: B 320 LEU cc_start: 0.7952 (pt) cc_final: 0.7512 (mt) REVERT: E 7 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8680 (tp) REVERT: F 83 TYR cc_start: 0.7521 (m-80) cc_final: 0.7122 (m-80) REVERT: F 98 GLU cc_start: 0.8507 (pm20) cc_final: 0.8082 (tt0) REVERT: G 1 MET cc_start: 0.9017 (mpp) cc_final: 0.8143 (ptp) REVERT: H 58 ASN cc_start: 0.7128 (m110) cc_final: 0.6888 (m-40) REVERT: H 76 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6381 (t80) REVERT: H 92 GLU cc_start: 0.7959 (pm20) cc_final: 0.7639 (tp30) REVERT: J 17 MET cc_start: 0.6438 (tmm) cc_final: 0.4935 (ptt) REVERT: J 45 MET cc_start: 0.0700 (mtt) cc_final: -0.0137 (ttt) REVERT: K 1 MET cc_start: 0.4231 (tpt) cc_final: 0.3463 (tmm) REVERT: C 73 MET cc_start: 0.6116 (mpp) cc_final: 0.5554 (mpp) REVERT: C 120 MET cc_start: 0.6208 (tmm) cc_final: 0.5684 (tmm) REVERT: C 177 PHE cc_start: 0.8472 (p90) cc_final: 0.8046 (p90) REVERT: C 370 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.4955 (pt0) REVERT: C 386 LEU cc_start: 0.2675 (OUTLIER) cc_final: 0.1391 (pp) REVERT: C 396 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7993 (pm20) REVERT: A 120 MET cc_start: 0.5744 (tmm) cc_final: 0.5139 (tmm) REVERT: A 347 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6133 (mtt180) REVERT: D 31 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5247 (pm20) REVERT: D 120 MET cc_start: 0.5579 (tmm) cc_final: 0.5072 (tmm) REVERT: D 189 ARG cc_start: 0.2975 (mtm180) cc_final: 0.2317 (mtm180) REVERT: D 254 GLU cc_start: 0.7810 (tt0) cc_final: 0.7371 (tp30) REVERT: D 304 LYS cc_start: 0.8155 (mptt) cc_final: 0.7574 (tptp) REVERT: D 317 LYS cc_start: 0.5396 (pttm) cc_final: 0.4775 (mtpt) outliers start: 58 outliers final: 49 residues processed: 282 average time/residue: 0.3295 time to fit residues: 137.7016 Evaluate side-chains 297 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.256300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.225232 restraints weight = 24674.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.224548 restraints weight = 35150.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.223748 restraints weight = 24976.333| |-----------------------------------------------------------------------------| r_work (final): 0.4838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5058 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18540 Z= 0.235 Angle : 0.717 14.954 25144 Z= 0.357 Chirality : 0.045 0.263 2669 Planarity : 0.005 0.057 3243 Dihedral : 5.285 44.083 2442 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.94 % Allowed : 21.25 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.17), residues: 2214 helix: -0.89 (0.27), residues: 372 sheet: -1.18 (0.20), residues: 593 loop : -1.27 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 307 HIS 0.013 0.001 HIS A 43 PHE 0.042 0.002 PHE F 77 TYR 0.045 0.002 TYR L 76 ARG 0.013 0.000 ARG I 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.57 seconds wall clock time: 73 minutes 51.42 seconds (4431.42 seconds total)