Starting phenix.real_space_refine on Tue Nov 19 01:24:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/11_2024/8sh2_40477.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/11_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_40477/11_2024/8sh2_40477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/11_2024/8sh2_40477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/11_2024/8sh2_40477.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh2_40477/11_2024/8sh2_40477.cif" } 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. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.46, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.4 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: 2.27 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: 6.44 Time building geometry restraints manager: 5.45 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: 0.00 - 2.97: 24342 2.97 - 5.94: 664 5.94 - 8.91: 95 8.91 - 11.88: 35 11.88 - 14.85: 8 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 3.040 nonbonded pdb=" O LYS J 80 " pdb=" OG1 THR J 84 " model vdw 2.329 3.040 nonbonded pdb=" O ARG G 9 " pdb=" OG1 THR G 12 " model vdw 2.353 3.040 nonbonded pdb=" OG1 THR C 288 " pdb=" OD1 ASP C 290 " model vdw 2.355 3.040 nonbonded pdb=" OG SER C 358 " pdb=" O GLN C 360 " model vdw 2.355 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.350 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: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 41.200 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 7 poor density : 444 time to evaluate : 1.962 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: 0.3399 time to fit residues: 222.3080 Evaluate side-chains 302 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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: 4.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 199 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS J 68 HIS K 10 HIS K 49 GLN L 58 ASN ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN 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 243 ASN ** 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 ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4397 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18540 Z= 0.420 Angle : 0.818 11.431 25144 Z= 0.428 Chirality : 0.050 0.234 2669 Planarity : 0.006 0.067 3243 Dihedral : 6.335 50.613 2444 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.43 % Allowed : 10.65 % Favored : 86.92 % 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: -2.52 (0.15), residues: 2214 helix: -2.05 (0.23), residues: 360 sheet: -1.14 (0.19), residues: 632 loop : -1.84 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 321 HIS 0.011 0.002 HIS D 109 PHE 0.033 0.003 PHE F 77 TYR 0.028 0.003 TYR D 163 ARG 0.027 0.001 ARG F 63 *********************** 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 372 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 2.156 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 121 LEU cc_start: 0.8238 (tp) cc_final: 0.8015 (tp) REVERT: B 147 LYS cc_start: 0.5498 (mttt) cc_final: 0.5115 (mttt) REVERT: B 228 ASN cc_start: 0.5549 (m-40) cc_final: 0.5250 (t0) REVERT: B 284 PHE cc_start: 0.6223 (t80) cc_final: 0.5956 (t80) REVERT: B 292 GLN cc_start: 0.9495 (tp-100) cc_final: 0.9044 (tm-30) REVERT: F 21 LEU cc_start: 0.9160 (tp) cc_final: 0.8781 (tp) REVERT: F 83 TYR cc_start: 0.7628 (m-80) cc_final: 0.6992 (m-80) REVERT: F 98 GLU cc_start: 0.8405 (pm20) cc_final: 0.8197 (tt0) REVERT: G 8 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8552 (mtm180) REVERT: H 45 MET cc_start: 0.7986 (ttt) cc_final: 0.7730 (ptm) REVERT: H 75 MET cc_start: 0.4976 (tmm) cc_final: 0.4496 (ppp) REVERT: H 83 TYR cc_start: 0.6575 (m-80) cc_final: 0.6079 (m-10) REVERT: H 105 MET cc_start: 0.6722 (tpt) cc_final: 0.5919 (mmp) REVERT: J 45 MET cc_start: 0.1155 (mtt) cc_final: 0.0172 (ttt) REVERT: K 23 THR cc_start: 0.8719 (p) cc_final: 0.8400 (t) REVERT: K 25 PHE cc_start: 0.9691 (m-80) cc_final: 0.9244 (m-80) REVERT: L 29 PHE cc_start: 0.6593 (m-80) cc_final: 0.6060 (m-80) REVERT: C 120 MET cc_start: 0.5979 (tmm) cc_final: 0.5366 (tmm) REVERT: C 121 LEU cc_start: 0.8778 (tp) cc_final: 0.8518 (tt) REVERT: C 177 PHE cc_start: 0.8090 (p90) cc_final: 0.7793 (p90) REVERT: C 233 PHE cc_start: 0.7247 (t80) cc_final: 0.6803 (t80) REVERT: C 369 LEU cc_start: 0.7322 (mt) cc_final: 0.7114 (mm) REVERT: C 386 LEU cc_start: 0.2490 (OUTLIER) cc_final: 0.1469 (pp) REVERT: A 119 TYR cc_start: 0.5007 (m-80) cc_final: 0.4736 (m-80) REVERT: A 120 MET cc_start: 0.5894 (tmm) cc_final: 0.5332 (tmm) REVERT: A 347 ARG cc_start: 0.6746 (mtt180) cc_final: 0.6223 (mtt180) REVERT: D 65 ARG cc_start: 0.7223 (ptm160) cc_final: 0.6615 (mtp-110) REVERT: D 144 SER cc_start: 0.4458 (OUTLIER) cc_final: 0.4003 (t) REVERT: D 228 ASN cc_start: 0.7555 (p0) cc_final: 0.7310 (m110) REVERT: D 254 GLU cc_start: 0.7867 (tt0) cc_final: 0.7528 (tp30) REVERT: D 304 LYS cc_start: 0.7887 (mptt) cc_final: 0.7621 (mptt) REVERT: D 317 LYS cc_start: 0.5118 (pttm) cc_final: 0.4453 (mttt) REVERT: D 328 ASP cc_start: 0.6670 (m-30) cc_final: 0.6300 (t0) REVERT: D 331 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6572 (mp0) outliers start: 48 outliers final: 28 residues processed: 349 average time/residue: 0.3572 time to fit residues: 180.6238 Evaluate side-chains 306 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 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 I residue 7 ILE 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 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 184 ASN 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: 30.0000 chunk 166 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN L 58 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 187 HIS ** 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 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 0.3662 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= 0.328 Angle : 0.733 9.895 25144 Z= 0.380 Chirality : 0.047 0.266 2669 Planarity : 0.005 0.071 3243 Dihedral : 6.065 49.963 2442 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.89 % Allowed : 13.54 % Favored : 83.57 % 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: -2.37 (0.16), residues: 2214 helix: -1.59 (0.24), residues: 371 sheet: -1.38 (0.19), residues: 622 loop : -1.64 (0.16), residues: 1221 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 0.034 0.002 PHE B 233 TYR 0.027 0.002 TYR D 163 ARG 0.006 0.001 ARG I 29 *********************** 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 356 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 2.058 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: 0.4995 (tpt) cc_final: 0.4511 (tpp) REVERT: B 121 LEU cc_start: 0.8492 (tp) cc_final: 0.7463 (tp) REVERT: B 130 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 145 LYS cc_start: 0.7007 (pttt) cc_final: 0.6793 (ptmt) REVERT: B 147 LYS cc_start: 0.5039 (mttt) cc_final: 0.4572 (mttt) REVERT: B 228 ASN cc_start: 0.5424 (m-40) cc_final: 0.5069 (t0) REVERT: B 284 PHE cc_start: 0.6143 (t80) cc_final: 0.5824 (t80) REVERT: B 292 GLN cc_start: 0.9497 (tp-100) cc_final: 0.9087 (tm-30) REVERT: E 8 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8601 (mtm-85) REVERT: F 72 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8310 (mttp) REVERT: F 83 TYR cc_start: 0.7638 (m-80) cc_final: 0.7031 (m-80) REVERT: G 68 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7806 (tpp80) REVERT: H 83 TYR cc_start: 0.6478 (m-80) cc_final: 0.6031 (m-10) REVERT: H 105 MET cc_start: 0.6780 (tpt) cc_final: 0.6079 (mmp) REVERT: J 17 MET cc_start: 0.6858 (tpp) cc_final: 0.5775 (tmm) REVERT: J 45 MET cc_start: 0.0863 (mtt) cc_final: -0.0098 (ttt) REVERT: K 23 THR cc_start: 0.8763 (p) cc_final: 0.8431 (t) REVERT: K 25 PHE cc_start: 0.9698 (m-80) cc_final: 0.9254 (m-80) REVERT: C 35 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5985 (p-80) REVERT: C 84 GLU cc_start: 0.8721 (pt0) cc_final: 0.8363 (pt0) REVERT: C 120 MET cc_start: 0.6192 (tmm) cc_final: 0.5567 (tmm) REVERT: C 177 PHE cc_start: 0.8156 (p90) cc_final: 0.7792 (p90) REVERT: C 369 LEU cc_start: 0.7286 (mt) cc_final: 0.7056 (mm) REVERT: C 370 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5841 (pt0) REVERT: C 385 CYS cc_start: 0.6162 (m) cc_final: 0.5842 (t) REVERT: C 386 LEU cc_start: 0.2611 (OUTLIER) cc_final: 0.1699 (pp) REVERT: C 396 GLN cc_start: 0.8288 (tm-30) cc_final: 0.8038 (pm20) REVERT: A 119 TYR cc_start: 0.5351 (m-80) cc_final: 0.5112 (m-80) REVERT: A 120 MET cc_start: 0.5870 (tmm) cc_final: 0.5263 (tmm) REVERT: A 347 ARG cc_start: 0.6703 (mtt180) cc_final: 0.6204 (mtt180) REVERT: D 144 SER cc_start: 0.3719 (OUTLIER) cc_final: 0.3313 (t) REVERT: D 228 ASN cc_start: 0.7737 (p0) cc_final: 0.7504 (m110) REVERT: D 254 GLU cc_start: 0.7828 (tt0) cc_final: 0.7458 (tp30) REVERT: D 291 LYS cc_start: 0.8606 (mttm) cc_final: 0.8383 (mmtp) REVERT: D 304 LYS cc_start: 0.8111 (mptt) cc_final: 0.7319 (tptm) REVERT: D 317 LYS cc_start: 0.5366 (pttm) cc_final: 0.4753 (mtpt) REVERT: D 328 ASP cc_start: 0.6772 (m-30) cc_final: 0.6394 (t0) REVERT: D 331 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6537 (mp0) outliers start: 57 outliers final: 31 residues processed: 329 average time/residue: 0.3519 time to fit residues: 169.3379 Evaluate side-chains 305 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 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 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 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain C residue 35 HIS 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 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN F 68 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** 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 114 ASN ** 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 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18540 Z= 0.320 Angle : 0.723 9.857 25144 Z= 0.372 Chirality : 0.046 0.236 2669 Planarity : 0.005 0.061 3243 Dihedral : 5.964 47.774 2442 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.80 % Allowed : 14.15 % Favored : 82.05 % 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: -2.29 (0.16), residues: 2214 helix: -1.36 (0.25), residues: 375 sheet: -1.57 (0.19), residues: 609 loop : -1.50 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 383 HIS 0.009 0.001 HIS B 110 PHE 0.046 0.002 PHE I 4 TYR 0.031 0.002 TYR L 76 ARG 0.013 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 357 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 282 time to evaluate : 2.335 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: B 103 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7451 (mm) REVERT: B 120 MET cc_start: 0.5091 (tpt) cc_final: 0.4797 (tpt) REVERT: B 121 LEU cc_start: 0.8504 (tp) cc_final: 0.8102 (tp) REVERT: B 145 LYS cc_start: 0.7145 (pttt) cc_final: 0.6928 (ptmt) REVERT: B 284 PHE cc_start: 0.6460 (t80) cc_final: 0.6248 (t80) REVERT: B 292 GLN cc_start: 0.9501 (tp-100) cc_final: 0.9096 (tm-30) REVERT: F 83 TYR cc_start: 0.7537 (m-80) cc_final: 0.7001 (m-80) REVERT: G 1 MET cc_start: 0.9109 (mpp) cc_final: 0.8304 (ptp) REVERT: H 45 MET cc_start: 0.8563 (ptm) cc_final: 0.8355 (ptp) REVERT: H 76 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6301 (t80) REVERT: H 83 TYR cc_start: 0.6595 (m-80) cc_final: 0.6137 (m-80) REVERT: H 105 MET cc_start: 0.6810 (tpt) cc_final: 0.6539 (tpt) REVERT: J 17 MET cc_start: 0.7184 (tpp) cc_final: 0.6368 (tmm) REVERT: J 45 MET cc_start: 0.1002 (mtt) cc_final: 0.0142 (ttt) REVERT: C 120 MET cc_start: 0.6356 (tmm) cc_final: 0.5763 (tmm) REVERT: C 177 PHE cc_start: 0.8272 (p90) cc_final: 0.7885 (p90) REVERT: C 342 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6461 (tt) REVERT: C 369 LEU cc_start: 0.7413 (mt) cc_final: 0.7184 (mm) REVERT: C 370 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5820 (pt0) REVERT: C 386 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.1541 (pp) REVERT: C 396 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7951 (pm20) REVERT: A 119 TYR cc_start: 0.5352 (m-80) cc_final: 0.5151 (m-80) REVERT: A 120 MET cc_start: 0.5904 (tmm) cc_final: 0.5239 (tmm) REVERT: A 196 HIS cc_start: 0.7979 (m90) cc_final: 0.7618 (m90) REVERT: A 271 HIS cc_start: 0.7168 (p-80) cc_final: 0.6828 (p90) REVERT: A 321 TRP cc_start: 0.6568 (OUTLIER) cc_final: 0.6245 (t-100) REVERT: A 328 ASP cc_start: 0.7456 (t0) cc_final: 0.7248 (t0) REVERT: A 347 ARG cc_start: 0.6665 (mtt180) cc_final: 0.6194 (mtt180) REVERT: D 144 SER cc_start: 0.3329 (OUTLIER) cc_final: 0.3005 (t) REVERT: D 254 GLU cc_start: 0.7838 (tt0) cc_final: 0.7449 (tp30) REVERT: D 304 LYS cc_start: 0.8143 (mptt) cc_final: 0.7401 (tptp) REVERT: D 317 LYS cc_start: 0.5477 (pttm) cc_final: 0.4814 (mtpt) REVERT: D 328 ASP cc_start: 0.6799 (m-30) cc_final: 0.6396 (t0) outliers start: 75 outliers final: 41 residues processed: 324 average time/residue: 0.3449 time to fit residues: 164.1823 Evaluate side-chains 310 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU 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 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 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 75 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 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 342 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 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 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 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 144 SER Chi-restraints excluded: chain D residue 184 ASN 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 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: 1.9990 chunk 120 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 146 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4414 moved from start: 0.4409 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= 0.233 Angle : 0.685 9.717 25144 Z= 0.346 Chirality : 0.045 0.225 2669 Planarity : 0.004 0.054 3243 Dihedral : 5.696 58.407 2442 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.04 % Allowed : 16.33 % Favored : 80.63 % 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: -2.14 (0.16), residues: 2214 helix: -1.17 (0.25), residues: 376 sheet: -1.49 (0.19), residues: 602 loop : -1.41 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 383 HIS 0.006 0.001 HIS D 271 PHE 0.034 0.002 PHE I 4 TYR 0.033 0.002 TYR L 76 ARG 0.007 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 336 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 2.556 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: B 103 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7396 (mm) REVERT: B 120 MET cc_start: 0.5120 (tpt) cc_final: 0.4816 (tpt) REVERT: B 121 LEU cc_start: 0.8621 (tp) cc_final: 0.8204 (tp) REVERT: B 145 LYS cc_start: 0.7169 (pttt) cc_final: 0.6947 (ptmt) REVERT: B 292 GLN cc_start: 0.9500 (tp-100) cc_final: 0.9130 (tm-30) REVERT: F 83 TYR cc_start: 0.7516 (m-80) cc_final: 0.7034 (m-80) REVERT: G 68 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7897 (tpp80) REVERT: H 83 TYR cc_start: 0.6385 (m-80) cc_final: 0.5913 (m-80) REVERT: H 90 ILE cc_start: 0.8006 (mp) cc_final: 0.7739 (mt) REVERT: H 105 MET cc_start: 0.6813 (tpt) cc_final: 0.6568 (tpt) REVERT: J 45 MET cc_start: 0.0846 (mtt) cc_final: -0.0010 (ttt) REVERT: C 120 MET cc_start: 0.6402 (tmm) cc_final: 0.5831 (tmm) REVERT: C 177 PHE cc_start: 0.8352 (p90) cc_final: 0.7961 (p90) REVERT: C 369 LEU cc_start: 0.7414 (mt) cc_final: 0.7189 (mm) REVERT: C 370 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5658 (pt0) REVERT: C 396 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7971 (pm20) REVERT: A 120 MET cc_start: 0.5907 (tmm) cc_final: 0.5246 (tmm) REVERT: A 196 HIS cc_start: 0.7912 (m90) cc_final: 0.7624 (m90) REVERT: A 271 HIS cc_start: 0.7248 (p-80) cc_final: 0.6994 (p90) REVERT: A 308 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4388 (mt) REVERT: A 321 TRP cc_start: 0.6593 (OUTLIER) cc_final: 0.5868 (t-100) REVERT: A 328 ASP cc_start: 0.7470 (t0) cc_final: 0.7240 (t0) REVERT: A 347 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6216 (mtt180) REVERT: D 144 SER cc_start: 0.3189 (OUTLIER) cc_final: 0.2821 (t) REVERT: D 254 GLU cc_start: 0.7765 (tt0) cc_final: 0.7374 (tp30) REVERT: D 304 LYS cc_start: 0.8177 (mptt) cc_final: 0.7441 (tptm) REVERT: D 317 LYS cc_start: 0.5400 (pttm) cc_final: 0.4786 (mtpt) REVERT: D 328 ASP cc_start: 0.6738 (m-30) cc_final: 0.6357 (t0) outliers start: 60 outliers final: 42 residues processed: 312 average time/residue: 0.3629 time to fit residues: 166.4651 Evaluate side-chains 307 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU 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 331 GLU 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 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 370 GLU 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 308 ILE Chi-restraints excluded: chain A residue 321 TRP 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 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: 5.9990 chunk 191 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 52 optimal weight: 0.4980 chunk 212 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4484 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18540 Z= 0.347 Angle : 0.745 10.614 25144 Z= 0.383 Chirality : 0.046 0.225 2669 Planarity : 0.005 0.056 3243 Dihedral : 5.827 47.056 2440 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.80 % Allowed : 16.84 % Favored : 79.36 % 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: -2.17 (0.17), residues: 2214 helix: -1.00 (0.26), residues: 376 sheet: -1.71 (0.19), residues: 627 loop : -1.36 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 307 HIS 0.008 0.001 HIS D 271 PHE 0.034 0.002 PHE F 77 TYR 0.031 0.003 TYR L 76 ARG 0.009 0.000 ARG I 29 *********************** 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 340 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 2.165 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: B 103 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7471 (mm) REVERT: B 120 MET cc_start: 0.5345 (tpt) cc_final: 0.5010 (tpt) REVERT: B 121 LEU cc_start: 0.8698 (tp) cc_final: 0.8263 (tp) REVERT: B 292 GLN cc_start: 0.9520 (tp-100) cc_final: 0.9158 (tm-30) REVERT: F 83 TYR cc_start: 0.7495 (m-80) cc_final: 0.7038 (m-80) REVERT: G 1 MET cc_start: 0.9204 (mpp) cc_final: 0.8441 (ptp) REVERT: H 33 ARG cc_start: 0.7723 (ttt-90) cc_final: 0.6619 (tpp80) REVERT: H 76 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6502 (t80) REVERT: H 83 TYR cc_start: 0.6478 (m-80) cc_final: 0.6210 (m-80) REVERT: H 105 MET cc_start: 0.7039 (tpt) cc_final: 0.6801 (tpt) REVERT: J 17 MET cc_start: 0.6373 (tmm) cc_final: 0.4610 (ptt) REVERT: J 45 MET cc_start: 0.0934 (mtt) cc_final: 0.0038 (ttt) REVERT: C 120 MET cc_start: 0.6541 (tmm) cc_final: 0.5919 (tmm) REVERT: C 177 PHE cc_start: 0.8351 (p90) cc_final: 0.7946 (p90) REVERT: C 369 LEU cc_start: 0.7530 (mt) cc_final: 0.7289 (mm) REVERT: C 370 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5583 (pt0) REVERT: C 396 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7985 (pm20) REVERT: A 112 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5712 (ttt-90) REVERT: A 120 MET cc_start: 0.5912 (tmm) cc_final: 0.5300 (tmm) REVERT: A 271 HIS cc_start: 0.7578 (p-80) cc_final: 0.7056 (p90) REVERT: A 273 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6645 (mp) REVERT: A 304 LYS cc_start: 0.6477 (mttp) cc_final: 0.6125 (mttp) REVERT: A 328 ASP cc_start: 0.7369 (t0) cc_final: 0.7127 (t0) REVERT: A 347 ARG cc_start: 0.6699 (mtt180) cc_final: 0.6225 (mtt180) REVERT: D 189 ARG cc_start: 0.2854 (mtm180) cc_final: 0.2232 (mtm180) REVERT: D 304 LYS cc_start: 0.8204 (mptt) cc_final: 0.7628 (tptp) REVERT: D 317 LYS cc_start: 0.5518 (pttm) cc_final: 0.4847 (mtpt) REVERT: D 328 ASP cc_start: 0.6960 (m-30) cc_final: 0.6421 (t0) outliers start: 75 outliers final: 50 residues processed: 311 average time/residue: 0.3514 time to fit residues: 162.1859 Evaluate side-chains 300 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 103 LEU 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 331 GLU 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 3 VAL 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 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 370 GLU 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 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 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 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 115 THR Chi-restraints excluded: chain D residue 144 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 155 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4437 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18540 Z= 0.236 Angle : 0.706 10.798 25144 Z= 0.354 Chirality : 0.044 0.219 2669 Planarity : 0.005 0.120 3243 Dihedral : 5.497 43.108 2440 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.99 % Allowed : 18.31 % Favored : 78.70 % 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: -0.99 (0.26), residues: 378 sheet: -1.55 (0.19), residues: 602 loop : -1.36 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 270 HIS 0.005 0.001 HIS C 43 PHE 0.032 0.002 PHE F 77 TYR 0.034 0.002 TYR L 76 ARG 0.015 0.001 ARG C 77 *********************** 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 317 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 2.227 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: B 103 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 120 MET cc_start: 0.5270 (tpt) cc_final: 0.4921 (tpt) REVERT: B 121 LEU cc_start: 0.8677 (tp) cc_final: 0.8228 (tp) REVERT: B 292 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9154 (tm-30) REVERT: F 83 TYR cc_start: 0.7474 (m-80) cc_final: 0.7010 (m-80) REVERT: G 1 MET cc_start: 0.9135 (mpp) cc_final: 0.8278 (ptp) REVERT: G 68 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7647 (tpp80) REVERT: H 33 ARG cc_start: 0.7677 (ttt-90) cc_final: 0.6557 (tpp80) REVERT: H 62 PHE cc_start: 0.6744 (m-10) cc_final: 0.6532 (m-10) REVERT: H 76 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6423 (t80) REVERT: H 105 MET cc_start: 0.7009 (tpt) cc_final: 0.6805 (tpt) REVERT: J 17 MET cc_start: 0.6319 (tmm) cc_final: 0.4631 (ptt) REVERT: C 120 MET cc_start: 0.6524 (tmm) cc_final: 0.5949 (tmm) REVERT: C 177 PHE cc_start: 0.8387 (p90) cc_final: 0.7988 (p90) REVERT: C 369 LEU cc_start: 0.7565 (mt) cc_final: 0.7332 (mm) REVERT: C 370 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5568 (pt0) REVERT: C 396 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7964 (pm20) REVERT: A 120 MET cc_start: 0.5879 (tmm) cc_final: 0.5229 (tmm) REVERT: A 170 LYS cc_start: 0.7122 (tppt) cc_final: 0.6905 (mmmt) REVERT: A 271 HIS cc_start: 0.7444 (p-80) cc_final: 0.7209 (p90) REVERT: A 304 LYS cc_start: 0.6484 (mttp) cc_final: 0.6132 (mttp) REVERT: A 328 ASP cc_start: 0.7413 (t0) cc_final: 0.7173 (t0) REVERT: A 347 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6194 (mtt180) REVERT: D 31 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: D 304 LYS cc_start: 0.8335 (mptt) cc_final: 0.7609 (tptp) REVERT: D 317 LYS cc_start: 0.5516 (pttm) cc_final: 0.4869 (mtpt) REVERT: D 328 ASP cc_start: 0.6940 (m-30) cc_final: 0.6435 (t0) REVERT: D 360 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6062 (tm-30) outliers start: 59 outliers final: 48 residues processed: 296 average time/residue: 0.3456 time to fit residues: 150.8730 Evaluate side-chains 304 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU 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 331 GLU 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 F residue 105 MET Chi-restraints excluded: chain G residue 3 VAL 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 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 370 GLU 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 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 115 THR Chi-restraints excluded: chain D residue 144 SER 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 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 GLN 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: 1.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 50.0000 chunk 41 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4432 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18540 Z= 0.223 Angle : 0.704 13.005 25144 Z= 0.350 Chirality : 0.044 0.223 2669 Planarity : 0.005 0.062 3243 Dihedral : 5.356 42.550 2440 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.89 % Allowed : 18.66 % Favored : 78.45 % 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: -1.97 (0.17), residues: 2214 helix: -0.91 (0.26), residues: 379 sheet: -1.45 (0.20), residues: 598 loop : -1.31 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 307 HIS 0.005 0.001 HIS D 271 PHE 0.028 0.002 PHE I 4 TYR 0.037 0.002 TYR L 76 ARG 0.010 0.000 ARG C 77 *********************** 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 317 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 120 MET cc_start: 0.5254 (tpt) cc_final: 0.4925 (tpt) REVERT: B 121 LEU cc_start: 0.8700 (tp) cc_final: 0.8256 (tp) REVERT: B 292 GLN cc_start: 0.9504 (tp-100) cc_final: 0.9163 (tm-30) REVERT: F 83 TYR cc_start: 0.7487 (m-80) cc_final: 0.7025 (m-80) REVERT: G 1 MET cc_start: 0.9097 (mpp) cc_final: 0.8255 (ptp) REVERT: H 33 ARG cc_start: 0.7671 (ttt-90) cc_final: 0.6590 (tpp80) REVERT: H 76 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6405 (t80) REVERT: J 17 MET cc_start: 0.6396 (tmm) cc_final: 0.4785 (ptt) REVERT: C 120 MET cc_start: 0.6544 (tmm) cc_final: 0.5974 (tmm) REVERT: C 177 PHE cc_start: 0.8412 (p90) cc_final: 0.8017 (p90) REVERT: C 369 LEU cc_start: 0.7566 (mt) cc_final: 0.7336 (mm) REVERT: C 370 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5533 (pt0) REVERT: C 396 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7943 (pm20) REVERT: A 120 MET cc_start: 0.5868 (tmm) cc_final: 0.5245 (tmm) REVERT: A 170 LYS cc_start: 0.7183 (tppt) cc_final: 0.6947 (mmmt) REVERT: A 196 HIS cc_start: 0.8108 (m90) cc_final: 0.7858 (m90) REVERT: A 271 HIS cc_start: 0.7487 (p-80) cc_final: 0.7167 (p90) REVERT: A 273 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6367 (mp) REVERT: A 304 LYS cc_start: 0.6498 (mttp) cc_final: 0.6104 (mttp) REVERT: A 328 ASP cc_start: 0.7415 (t0) cc_final: 0.7154 (t0) REVERT: A 344 VAL cc_start: 0.6946 (OUTLIER) cc_final: 0.6591 (m) REVERT: A 347 ARG cc_start: 0.6679 (mtt180) cc_final: 0.6129 (mtt180) REVERT: D 31 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5373 (pm20) REVERT: D 189 ARG cc_start: 0.3010 (mtm180) cc_final: 0.2331 (mtm180) REVERT: D 304 LYS cc_start: 0.8357 (mptt) cc_final: 0.7652 (tptp) REVERT: D 317 LYS cc_start: 0.5509 (pttm) cc_final: 0.4882 (mtpt) REVERT: D 360 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.5943 (tm-30) outliers start: 57 outliers final: 44 residues processed: 295 average time/residue: 0.3571 time to fit residues: 152.5305 Evaluate side-chains 298 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU 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 331 GLU 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 88 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 LEU 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 C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 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 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 A residue 344 VAL 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 252 THR 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 360 GLN 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: 1.9990 chunk 185 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 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 116 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4451 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18540 Z= 0.260 Angle : 0.729 12.030 25144 Z= 0.367 Chirality : 0.045 0.257 2669 Planarity : 0.005 0.051 3243 Dihedral : 5.396 42.601 2440 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.89 % Allowed : 18.97 % Favored : 78.14 % 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: -1.93 (0.17), residues: 2214 helix: -0.99 (0.26), residues: 378 sheet: -1.37 (0.20), residues: 595 loop : -1.28 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 270 HIS 0.011 0.001 HIS D 271 PHE 0.040 0.002 PHE F 77 TYR 0.038 0.002 TYR L 76 ARG 0.014 0.001 ARG D 238 *********************** 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 305 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 2.083 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 103 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7159 (mm) REVERT: B 120 MET cc_start: 0.5310 (tpt) cc_final: 0.4958 (tpt) REVERT: B 121 LEU cc_start: 0.8740 (tp) cc_final: 0.8296 (tp) REVERT: B 292 GLN cc_start: 0.9509 (tp-100) cc_final: 0.9165 (tm-30) REVERT: F 83 TYR cc_start: 0.7523 (m-80) cc_final: 0.7070 (m-80) REVERT: H 33 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.6606 (tpp80) REVERT: H 76 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6487 (t80) REVERT: J 17 MET cc_start: 0.6458 (tmm) cc_final: 0.4881 (ptt) REVERT: K 1 MET cc_start: 0.4528 (tpt) cc_final: 0.3227 (ttt) REVERT: C 120 MET cc_start: 0.6597 (tmm) cc_final: 0.6014 (tmm) REVERT: C 177 PHE cc_start: 0.8424 (p90) cc_final: 0.8032 (p90) REVERT: C 369 LEU cc_start: 0.7627 (mt) cc_final: 0.7394 (mm) REVERT: C 370 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5256 (pt0) REVERT: C 396 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7947 (pm20) REVERT: A 120 MET cc_start: 0.5798 (tmm) cc_final: 0.5194 (tmm) REVERT: A 170 LYS cc_start: 0.7143 (tppt) cc_final: 0.6892 (mmmt) REVERT: A 196 HIS cc_start: 0.8204 (m90) cc_final: 0.7934 (m90) REVERT: A 271 HIS cc_start: 0.7570 (p-80) cc_final: 0.7263 (p90) REVERT: A 273 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6537 (mp) REVERT: A 304 LYS cc_start: 0.6478 (mttp) cc_final: 0.6122 (mttp) REVERT: A 328 ASP cc_start: 0.7381 (t0) cc_final: 0.7134 (t0) REVERT: A 344 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6607 (m) REVERT: A 347 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6125 (mtt180) REVERT: D 31 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5386 (pm20) REVERT: D 189 ARG cc_start: 0.3016 (mtm180) cc_final: 0.2311 (mtm180) REVERT: D 304 LYS cc_start: 0.8364 (mptt) cc_final: 0.7687 (tptp) REVERT: D 317 LYS cc_start: 0.5529 (pttm) cc_final: 0.4892 (mtpt) REVERT: D 360 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.5921 (tm-30) outliers start: 57 outliers final: 45 residues processed: 285 average time/residue: 0.3475 time to fit residues: 145.1536 Evaluate side-chains 289 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU 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 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 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 LEU 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 232 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 370 GLU 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 273 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 344 VAL 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 115 THR 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 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 GLN 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: 20.0000 chunk 99 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 chunk 201 optimal weight: 0.1980 chunk 174 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 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 116 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4440 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18540 Z= 0.245 Angle : 0.733 12.438 25144 Z= 0.367 Chirality : 0.045 0.215 2669 Planarity : 0.005 0.061 3243 Dihedral : 5.350 41.327 2440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.84 % Allowed : 19.47 % Favored : 77.69 % 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: -1.93 (0.17), residues: 2214 helix: -1.02 (0.26), residues: 380 sheet: -1.36 (0.20), residues: 588 loop : -1.28 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 307 HIS 0.011 0.001 HIS D 271 PHE 0.040 0.002 PHE F 77 TYR 0.038 0.002 TYR L 76 ARG 0.014 0.001 ARG H 82 ********************** 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 302 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.861 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 103 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 120 MET cc_start: 0.5299 (tpt) cc_final: 0.4940 (tpt) REVERT: B 121 LEU cc_start: 0.8749 (tp) cc_final: 0.8309 (tp) REVERT: B 229 ARG cc_start: 0.7205 (ttm110) cc_final: 0.6954 (mmm-85) REVERT: B 292 GLN cc_start: 0.9506 (tp-100) cc_final: 0.9156 (tm-30) REVERT: B 320 LEU cc_start: 0.8043 (pt) cc_final: 0.7616 (mt) REVERT: F 43 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8519 (mppt) REVERT: F 83 TYR cc_start: 0.7520 (m-80) cc_final: 0.7107 (m-80) REVERT: G 1 MET cc_start: 0.8933 (mpp) cc_final: 0.8019 (ptp) REVERT: H 33 ARG cc_start: 0.7737 (ttt-90) cc_final: 0.6646 (tpp80) REVERT: H 45 MET cc_start: 0.8373 (ptp) cc_final: 0.7915 (pmm) REVERT: H 76 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6535 (t80) REVERT: J 17 MET cc_start: 0.6448 (tmm) cc_final: 0.4937 (ptt) REVERT: K 1 MET cc_start: 0.4712 (tpt) cc_final: 0.3538 (ttt) REVERT: L 75 MET cc_start: 0.6453 (ptp) cc_final: 0.5843 (ptp) REVERT: C 120 MET cc_start: 0.6603 (tmm) cc_final: 0.6026 (tmm) REVERT: C 177 PHE cc_start: 0.8447 (p90) cc_final: 0.8056 (p90) REVERT: C 369 LEU cc_start: 0.7597 (mt) cc_final: 0.7365 (mm) REVERT: C 370 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5178 (pt0) REVERT: C 396 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7935 (pm20) REVERT: A 78 TRP cc_start: 0.2796 (m100) cc_final: 0.2390 (m-10) REVERT: A 120 MET cc_start: 0.5903 (tmm) cc_final: 0.5269 (tmm) REVERT: A 196 HIS cc_start: 0.8185 (m90) cc_final: 0.7925 (m90) REVERT: A 273 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6606 (mp) REVERT: A 304 LYS cc_start: 0.6474 (mttp) cc_final: 0.6116 (mttp) REVERT: A 328 ASP cc_start: 0.7415 (t0) cc_final: 0.7164 (t0) REVERT: A 344 VAL cc_start: 0.6999 (OUTLIER) cc_final: 0.6662 (m) REVERT: A 347 ARG cc_start: 0.6633 (mtt180) cc_final: 0.6100 (mtt180) REVERT: D 31 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5351 (pm20) REVERT: D 189 ARG cc_start: 0.3043 (mtm180) cc_final: 0.2319 (mtm180) REVERT: D 304 LYS cc_start: 0.8378 (mptt) cc_final: 0.7699 (tptp) REVERT: D 317 LYS cc_start: 0.5471 (pttm) cc_final: 0.4888 (mtpt) REVERT: D 360 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.5912 (tm-30) outliers start: 56 outliers final: 44 residues processed: 281 average time/residue: 0.3494 time to fit residues: 143.6895 Evaluate side-chains 291 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 103 LEU 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 8 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 3 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 370 GLU 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 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 320 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 344 VAL 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 115 THR 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 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 GLN 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: 0.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 179 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 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** 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 = 0.256542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.232083 restraints weight = 24704.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.224988 restraints weight = 30398.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.225213 restraints weight = 30912.981| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18540 Z= 0.239 Angle : 0.734 12.452 25144 Z= 0.368 Chirality : 0.045 0.320 2669 Planarity : 0.005 0.055 3243 Dihedral : 5.324 40.968 2440 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.89 % Allowed : 19.73 % Favored : 77.38 % 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: -1.88 (0.17), residues: 2214 helix: -1.07 (0.26), residues: 382 sheet: -1.27 (0.20), residues: 582 loop : -1.24 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 307 HIS 0.009 0.001 HIS D 271 PHE 0.042 0.002 PHE F 77 TYR 0.037 0.002 TYR L 76 ARG 0.012 0.001 ARG D 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.93 seconds wall clock time: 77 minutes 32.48 seconds (4652.48 seconds total)