Starting phenix.real_space_refine on Mon Jan 20 22:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5a_45209/01_2025/9c5a_45209.cif" } resolution = 4.2 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= 0.022 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 10114 2.51 5 N 2688 2.21 5 O 2928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15806 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain breaks: 2 Chain: "M" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3309 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 391} Chain: "C" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1447 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 62 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: c, b, m, Y Time building chain proxies: 12.50, per 1000 atoms: 0.79 Number of scatterers: 15806 At special positions: 0 Unit cell: (92.046, 189.382, 93.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 2928 8.00 N 2688 7.00 C 10114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 50.8% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.656A pdb=" N ALA B 88 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 160 Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.520A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 5.001A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.219A pdb=" N HIS B 223 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 237 through 256 removed outlier: 3.532A pdb=" N VAL B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.939A pdb=" N GLY B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.764A pdb=" N LEU B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 362 removed outlier: 3.772A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 376 removed outlier: 6.429A pdb=" N GLY B 366 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Proline residue: B 370 - end of helix removed outlier: 5.747A pdb=" N LYS B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 401 through 415 removed outlier: 4.263A pdb=" N ARG B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 645 through 649 Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 28 through 38 removed outlier: 4.143A pdb=" N PHE M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 45 removed outlier: 4.044A pdb=" N VAL M 45 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 95 Processing helix chain 'M' and resid 98 through 116 removed outlier: 6.454A pdb=" N VAL M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE M 108 " --> pdb=" O ASP M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 134 removed outlier: 4.600A pdb=" N GLU M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 149 removed outlier: 3.526A pdb=" N ILE M 147 " --> pdb=" O VAL M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 163 Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 238 through 245 removed outlier: 3.625A pdb=" N TRP M 242 " --> pdb=" O ARG M 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 135 through 144 Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'b' and resid 41 through 53 Processing helix chain 'b' and resid 55 through 72 Processing helix chain 'b' and resid 76 through 78 No H-bonds generated for 'chain 'b' and resid 76 through 78' Processing helix chain 'b' and resid 79 through 84 Processing helix chain 'b' and resid 85 through 89 removed outlier: 3.657A pdb=" N ALA b 88 " --> pdb=" O LYS b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 106 Processing helix chain 'b' and resid 109 through 115 Processing helix chain 'b' and resid 117 through 124 Processing helix chain 'b' and resid 128 through 141 Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 147 through 160 Processing helix chain 'b' and resid 163 through 181 Processing helix chain 'b' and resid 184 through 197 removed outlier: 3.521A pdb=" N LYS b 197 " --> pdb=" O GLU b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 200 through 215 removed outlier: 5.002A pdb=" N SER b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 218 through 224 removed outlier: 4.217A pdb=" N HIS b 223 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS b 224 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 225 through 233 Processing helix chain 'b' and resid 237 through 256 removed outlier: 3.530A pdb=" N VAL b 243 " --> pdb=" O TRP b 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR b 254 " --> pdb=" O ARG b 250 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 305 Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 312 through 327 Processing helix chain 'b' and resid 328 through 334 removed outlier: 4.939A pdb=" N GLY b 333 " --> pdb=" O SER b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 343 removed outlier: 3.764A pdb=" N LEU b 343 " --> pdb=" O LEU b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 362 removed outlier: 3.771A pdb=" N ILE b 362 " --> pdb=" O ALA b 358 " (cutoff:3.500A) Processing helix chain 'b' and resid 363 through 376 removed outlier: 6.430A pdb=" N GLY b 366 " --> pdb=" O GLN b 363 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU b 369 " --> pdb=" O GLY b 366 " (cutoff:3.500A) Proline residue: b 370 - end of helix removed outlier: 5.748A pdb=" N LYS b 373 " --> pdb=" O PRO b 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 382 through 397 Processing helix chain 'b' and resid 401 through 415 removed outlier: 4.263A pdb=" N ARG b 407 " --> pdb=" O SER b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 417 through 427 Processing helix chain 'b' and resid 621 through 627 Processing helix chain 'b' and resid 645 through 649 Processing helix chain 'm' and resid 25 through 27 No H-bonds generated for 'chain 'm' and resid 25 through 27' Processing helix chain 'm' and resid 28 through 38 removed outlier: 4.143A pdb=" N PHE m 32 " --> pdb=" O VAL m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 45 removed outlier: 4.043A pdb=" N VAL m 45 " --> pdb=" O VAL m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 75 through 95 Processing helix chain 'm' and resid 98 through 116 removed outlier: 6.454A pdb=" N VAL m 107 " --> pdb=" O LYS m 103 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE m 108 " --> pdb=" O ASP m 104 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 134 removed outlier: 4.600A pdb=" N GLU m 132 " --> pdb=" O ASN m 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 149 removed outlier: 3.527A pdb=" N ILE m 147 " --> pdb=" O VAL m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 158 through 163 Processing helix chain 'm' and resid 224 through 226 No H-bonds generated for 'chain 'm' and resid 224 through 226' Processing helix chain 'm' and resid 238 through 245 removed outlier: 3.626A pdb=" N TRP m 242 " --> pdb=" O ARG m 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 13 Processing helix chain 'c' and resid 29 through 39 Processing helix chain 'c' and resid 74 through 82 Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 99 through 112 Processing helix chain 'c' and resid 113 through 117 Processing helix chain 'c' and resid 135 through 144 Processing helix chain 'c' and resid 145 through 148 Processing helix chain 'c' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 removed outlier: 5.845A pdb=" N ILE M 14 " --> pdb=" O ASN M 9 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN M 9 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER M 4 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'M' and resid 228 through 233 removed outlier: 3.861A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 179 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL M 405 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE M 181 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR M 407 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 183 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR M 409 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU M 185 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA M 411 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE M 187 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS M 413 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE M 377 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS M 413 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE M 375 " --> pdb=" O LYS M 413 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU M 373 " --> pdb=" O GLN M 415 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN M 374 " --> pdb=" O VAL M 310 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL M 310 " --> pdb=" O ASN M 374 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN M 376 " --> pdb=" O ILE M 308 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE M 308 " --> pdb=" O GLN M 376 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU M 306 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS M 345 " --> pdb=" O GLU M 306 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE M 308 " --> pdb=" O VAL M 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 228 through 233 removed outlier: 3.861A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 179 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL M 405 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE M 181 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR M 407 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 183 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR M 409 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU M 185 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA M 411 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE M 187 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS M 413 " --> pdb=" O ILE M 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 248 through 250 removed outlier: 6.415A pdb=" N SER M 219 " --> pdb=" O LEU M 392 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 392 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER M 221 " --> pdb=" O ASN M 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 274 through 281 removed outlier: 6.257A pdb=" N SER M 353 " --> pdb=" O PRO M 325 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS M 355 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU M 323 " --> pdb=" O LYS M 355 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 357 " --> pdb=" O MET M 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET M 321 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN M 359 " --> pdb=" O LEU M 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 58 removed outlier: 4.913A pdb=" N GLY C 24 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY C 87 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ASP C 93 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 121 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN C 156 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 14 through 19 removed outlier: 5.845A pdb=" N ILE m 14 " --> pdb=" O ASN m 9 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN m 9 " --> pdb=" O ILE m 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER m 4 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 117 through 118 Processing sheet with id=AB1, first strand: chain 'm' and resid 228 through 233 removed outlier: 3.860A pdb=" N ASP m 230 " --> pdb=" O ARG m 263 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN m 256 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE m 210 " --> pdb=" O ASN m 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG m 258 " --> pdb=" O ALA m 208 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA m 208 " --> pdb=" O ARG m 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE m 202 " --> pdb=" O VAL m 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA m 179 " --> pdb=" O LYS m 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL m 405 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE m 181 " --> pdb=" O VAL m 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR m 407 " --> pdb=" O PHE m 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL m 183 " --> pdb=" O TYR m 407 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR m 409 " --> pdb=" O VAL m 183 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU m 185 " --> pdb=" O THR m 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA m 411 " --> pdb=" O GLU m 185 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE m 187 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS m 413 " --> pdb=" O ILE m 187 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE m 377 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS m 413 " --> pdb=" O ILE m 375 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE m 375 " --> pdb=" O LYS m 413 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN m 415 " --> pdb=" O LEU m 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU m 373 " --> pdb=" O GLN m 415 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN m 374 " --> pdb=" O VAL m 310 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL m 310 " --> pdb=" O ASN m 374 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN m 376 " --> pdb=" O ILE m 308 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE m 308 " --> pdb=" O GLN m 376 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU m 306 " --> pdb=" O LYS m 345 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS m 345 " --> pdb=" O GLU m 306 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE m 308 " --> pdb=" O VAL m 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 228 through 233 removed outlier: 3.860A pdb=" N ASP m 230 " --> pdb=" O ARG m 263 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN m 256 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE m 210 " --> pdb=" O ASN m 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG m 258 " --> pdb=" O ALA m 208 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA m 208 " --> pdb=" O ARG m 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE m 202 " --> pdb=" O VAL m 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA m 179 " --> pdb=" O LYS m 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL m 405 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE m 181 " --> pdb=" O VAL m 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR m 407 " --> pdb=" O PHE m 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL m 183 " --> pdb=" O TYR m 407 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR m 409 " --> pdb=" O VAL m 183 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU m 185 " --> pdb=" O THR m 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA m 411 " --> pdb=" O GLU m 185 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE m 187 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS m 413 " --> pdb=" O ILE m 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 248 through 250 removed outlier: 6.415A pdb=" N SER m 219 " --> pdb=" O LEU m 392 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU m 392 " --> pdb=" O SER m 219 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER m 221 " --> pdb=" O ASN m 390 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 274 through 281 removed outlier: 6.258A pdb=" N SER m 353 " --> pdb=" O PRO m 325 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS m 355 " --> pdb=" O LEU m 323 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU m 323 " --> pdb=" O LYS m 355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 357 " --> pdb=" O MET m 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET m 321 " --> pdb=" O LEU m 357 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN m 359 " --> pdb=" O LEU m 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 51 through 58 removed outlier: 4.913A pdb=" N GLY c 24 " --> pdb=" O VAL c 68 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY c 87 " --> pdb=" O GLU c 17 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG c 19 " --> pdb=" O GLY c 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE c 89 " --> pdb=" O ARG c 19 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU c 21 " --> pdb=" O ILE c 89 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL c 91 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL c 23 " --> pdb=" O VAL c 91 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ASP c 93 " --> pdb=" O VAL c 23 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU c 121 " --> pdb=" O TYR c 154 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN c 156 " --> pdb=" O LEU c 121 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL c 123 " --> pdb=" O GLN c 156 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.44: 3570 1.44 - 1.57: 8832 1.57 - 1.69: 10 1.69 - 1.81: 118 Bond restraints: 16108 Sorted by residual: bond pdb=" CA ILE b 174 " pdb=" C ILE b 174 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.22e-02 6.72e+03 1.38e+01 bond pdb=" CA ILE B 174 " pdb=" C ILE B 174 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.22e-02 6.72e+03 1.38e+01 bond pdb=" CA ARG b 132 " pdb=" C ARG b 132 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.27e-02 6.20e+03 1.35e+01 bond pdb=" CA ARG B 132 " pdb=" C ARG B 132 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.27e-02 6.20e+03 1.34e+01 bond pdb=" CA ASN M 105 " pdb=" CB ASN M 105 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.35e-02 5.49e+03 1.19e+01 ... (remaining 16103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 19347 2.14 - 4.28: 2064 4.28 - 6.42: 297 6.42 - 8.56: 92 8.56 - 10.69: 22 Bond angle restraints: 21822 Sorted by residual: angle pdb=" C ASP b 181 " pdb=" N PRO b 182 " pdb=" CA PRO b 182 " ideal model delta sigma weight residual 119.56 129.06 -9.50 1.02e+00 9.61e-01 8.67e+01 angle pdb=" C ASP B 181 " pdb=" N PRO B 182 " pdb=" CA PRO B 182 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.02e+00 9.61e-01 8.62e+01 angle pdb=" C ASP B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 119.56 129.00 -9.44 1.02e+00 9.61e-01 8.57e+01 angle pdb=" C ASP b 645 " pdb=" N PRO b 646 " pdb=" CA PRO b 646 " ideal model delta sigma weight residual 119.56 128.94 -9.38 1.02e+00 9.61e-01 8.47e+01 angle pdb=" C LEU c 130 " pdb=" N PRO c 131 " pdb=" CA PRO c 131 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.02e+00 9.61e-01 7.61e+01 ... (remaining 21817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9702 35.81 - 71.61: 108 71.61 - 107.42: 18 107.42 - 143.22: 4 143.22 - 179.03: 4 Dihedral angle restraints: 9836 sinusoidal: 4034 harmonic: 5802 Sorted by residual: dihedral pdb=" O3B GTP c1001 " pdb=" O3A GTP c1001 " pdb=" PB GTP c1001 " pdb=" PA GTP c1001 " ideal model delta sinusoidal sigma weight residual -68.92 110.10 -179.03 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PB GTP C1001 " pdb=" PA GTP C1001 " ideal model delta sinusoidal sigma weight residual -68.92 110.06 -178.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP C1001 " pdb=" C1' GTP C1001 " pdb=" N9 GTP C1001 " pdb=" O4' GTP C1001 " ideal model delta sinusoidal sigma weight residual 104.59 -70.81 175.40 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 9833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1373 0.054 - 0.109: 836 0.109 - 0.163: 254 0.163 - 0.217: 53 0.217 - 0.271: 8 Chirality restraints: 2524 Sorted by residual: chirality pdb=" CA LYS m 21 " pdb=" N LYS m 21 " pdb=" C LYS m 21 " pdb=" CB LYS m 21 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS M 21 " pdb=" N LYS M 21 " pdb=" C LYS M 21 " pdb=" CB LYS M 21 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA SER B 118 " pdb=" N SER B 118 " pdb=" C SER B 118 " pdb=" CB SER B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2521 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE y 417 " -0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C ILE y 417 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE y 417 " -0.035 2.00e-02 2.50e+03 pdb=" OXT ILE y 417 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 417 " 0.028 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C ILE Y 417 " -0.098 2.00e-02 2.50e+03 pdb=" O ILE Y 417 " 0.035 2.00e-02 2.50e+03 pdb=" OXT ILE Y 417 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 275 " 0.033 2.00e-02 2.50e+03 1.74e-02 6.09e+00 pdb=" CG TYR M 275 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR M 275 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR M 275 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR M 275 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR M 275 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 275 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR M 275 " 0.024 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 51 2.49 - 3.09: 12930 3.09 - 3.69: 24298 3.69 - 4.30: 37073 4.30 - 4.90: 58123 Nonbonded interactions: 132475 Sorted by model distance: nonbonded pdb=" OG1 THR c 31 " pdb="MG MG c1000 " model vdw 1.887 2.170 nonbonded pdb=" OG1 THR C 31 " pdb="MG MG C1000 " model vdw 1.887 2.170 nonbonded pdb="MG MG C1000 " pdb=" O2G GTP C1001 " model vdw 1.940 2.170 nonbonded pdb="MG MG c1000 " pdb=" O2G GTP c1001 " model vdw 1.940 2.170 nonbonded pdb=" O ARG b 344 " pdb=" NH1 ARG b 344 " model vdw 2.158 3.120 ... (remaining 132470 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: 0.08 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'y' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.014 0.064 16108 Z= 0.916 Angle : 1.485 10.695 21822 Z= 1.030 Chirality : 0.073 0.271 2524 Planarity : 0.005 0.057 2752 Dihedral : 12.262 179.025 6064 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 0.45 % Allowed : 0.00 % Favored : 99.55 % 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: 0.19 (0.19), residues: 1954 helix: -0.39 (0.16), residues: 814 sheet: 0.07 (0.26), residues: 356 loop : 1.10 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP C 153 HIS 0.008 0.002 HIS b 624 PHE 0.025 0.004 PHE C 124 TYR 0.033 0.005 TYR M 275 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 828 time to evaluate : 1.853 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: symmetry clash REVERT: B 43 LYS cc_start: 0.8347 (mttt) cc_final: 0.7774 (mmmt) REVERT: B 50 MET cc_start: 0.8532 (mtm) cc_final: 0.8140 (mpp) REVERT: B 51 LEU cc_start: 0.8621 (mt) cc_final: 0.8294 (mt) REVERT: B 54 ASN cc_start: 0.7812 (p0) cc_final: 0.7578 (t0) REVERT: B 55 LYS cc_start: 0.8314 (ttpt) cc_final: 0.8015 (mtpt) REVERT: B 59 LYS cc_start: 0.8531 (mttm) cc_final: 0.8262 (mttp) REVERT: B 63 MET cc_start: 0.8436 (mmm) cc_final: 0.8059 (mmm) REVERT: B 64 LYS cc_start: 0.9111 (mttt) cc_final: 0.8690 (mtpp) REVERT: B 72 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8579 (mtmt) REVERT: B 74 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8237 (mmtt) REVERT: B 83 VAL cc_start: 0.8651 (t) cc_final: 0.8447 (t) REVERT: B 85 LYS cc_start: 0.8733 (mttt) cc_final: 0.8344 (mttt) REVERT: B 89 SER cc_start: 0.8248 (t) cc_final: 0.8011 (t) REVERT: B 91 ASN cc_start: 0.6673 (t0) cc_final: 0.5815 (t0) REVERT: B 94 ILE cc_start: 0.8327 (mt) cc_final: 0.8091 (mt) REVERT: B 97 LEU cc_start: 0.8836 (mt) cc_final: 0.8405 (mm) REVERT: B 101 TYR cc_start: 0.8557 (t80) cc_final: 0.8257 (t80) REVERT: B 120 PHE cc_start: 0.8398 (m-80) cc_final: 0.8090 (m-10) REVERT: B 121 GLN cc_start: 0.8390 (tt0) cc_final: 0.8162 (mt0) REVERT: B 125 LYS cc_start: 0.8703 (mttt) cc_final: 0.8365 (mtpp) REVERT: B 132 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8132 (ttm170) REVERT: B 137 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7656 (mtp-110) REVERT: B 141 SER cc_start: 0.8461 (m) cc_final: 0.8008 (t) REVERT: B 165 TYR cc_start: 0.8540 (t80) cc_final: 0.8272 (t80) REVERT: B 175 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 177 LEU cc_start: 0.8597 (tp) cc_final: 0.8296 (tp) REVERT: B 181 ASP cc_start: 0.8067 (t0) cc_final: 0.7742 (t0) REVERT: B 185 LYS cc_start: 0.7854 (tttt) cc_final: 0.7288 (ttpp) REVERT: B 190 GLU cc_start: 0.8063 (tt0) cc_final: 0.7116 (tt0) REVERT: B 191 VAL cc_start: 0.8990 (t) cc_final: 0.8222 (t) REVERT: B 194 LYS cc_start: 0.8887 (mttt) cc_final: 0.8319 (mttt) REVERT: B 196 LEU cc_start: 0.8478 (mt) cc_final: 0.8163 (tp) REVERT: B 215 CYS cc_start: 0.7816 (t) cc_final: 0.7122 (t) REVERT: B 226 TYR cc_start: 0.7785 (t80) cc_final: 0.7572 (t80) REVERT: B 241 GLN cc_start: 0.8461 (mt0) cc_final: 0.7636 (mt0) REVERT: B 244 ILE cc_start: 0.9113 (mt) cc_final: 0.8686 (tp) REVERT: B 246 HIS cc_start: 0.8442 (m-70) cc_final: 0.7724 (m-70) REVERT: B 247 MET cc_start: 0.7401 (tmm) cc_final: 0.7077 (tmm) REVERT: B 298 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7966 (mpt180) REVERT: B 305 LYS cc_start: 0.9012 (tttt) cc_final: 0.8797 (ttpp) REVERT: B 311 ARG cc_start: 0.8182 (ptt180) cc_final: 0.7702 (ptt-90) REVERT: B 317 MET cc_start: 0.8603 (tpp) cc_final: 0.8298 (tpt) REVERT: B 324 TRP cc_start: 0.8683 (t-100) cc_final: 0.8415 (t-100) REVERT: B 326 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7795 (mm) REVERT: B 341 ARG cc_start: 0.8771 (ptt90) cc_final: 0.7908 (ttp-110) REVERT: B 417 ASP cc_start: 0.8032 (t0) cc_final: 0.7538 (m-30) REVERT: B 635 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 640 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8374 (Cg_endo) REVERT: B 641 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8169 (pm20) REVERT: M 15 PHE cc_start: 0.7944 (t80) cc_final: 0.7681 (t80) REVERT: M 16 LEU cc_start: 0.8681 (tt) cc_final: 0.8384 (tp) REVERT: M 17 GLU cc_start: 0.7704 (pt0) cc_final: 0.7463 (pt0) REVERT: M 21 LYS cc_start: 0.8513 (mttt) cc_final: 0.7786 (mttp) REVERT: M 30 ASP cc_start: 0.8314 (m-30) cc_final: 0.7975 (t0) REVERT: M 33 PHE cc_start: 0.8449 (m-80) cc_final: 0.8101 (m-80) REVERT: M 34 GLU cc_start: 0.8900 (tt0) cc_final: 0.8527 (tt0) REVERT: M 36 GLN cc_start: 0.8486 (tp40) cc_final: 0.8264 (tp40) REVERT: M 43 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7412 (mt-10) REVERT: M 44 ASN cc_start: 0.8121 (t0) cc_final: 0.7509 (t0) REVERT: M 60 TYR cc_start: 0.8409 (t80) cc_final: 0.8180 (t80) REVERT: M 78 PHE cc_start: 0.9077 (t80) cc_final: 0.8805 (t80) REVERT: M 81 GLU cc_start: 0.7360 (tp30) cc_final: 0.6821 (tp30) REVERT: M 108 ILE cc_start: 0.8854 (mt) cc_final: 0.8638 (mt) REVERT: M 115 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7775 (tp30) REVERT: M 116 MET cc_start: 0.7833 (mtm) cc_final: 0.7265 (mtm) REVERT: M 119 ASN cc_start: 0.8320 (t0) cc_final: 0.7520 (t0) REVERT: M 126 GLU cc_start: 0.8076 (tp30) cc_final: 0.7785 (tp30) REVERT: M 134 ILE cc_start: 0.8158 (mt) cc_final: 0.7495 (mt) REVERT: M 135 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8207 (mmtt) REVERT: M 157 LEU cc_start: 0.8353 (mt) cc_final: 0.8084 (mt) REVERT: M 159 THR cc_start: 0.8251 (m) cc_final: 0.7984 (t) REVERT: M 173 LYS cc_start: 0.7479 (tttt) cc_final: 0.7155 (tttt) REVERT: M 181 PHE cc_start: 0.8115 (m-80) cc_final: 0.7592 (m-80) REVERT: M 182 ASP cc_start: 0.6599 (m-30) cc_final: 0.6068 (m-30) REVERT: M 183 VAL cc_start: 0.8071 (t) cc_final: 0.7672 (p) REVERT: M 203 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7045 (mm-40) REVERT: M 209 CYS cc_start: 0.7655 (t) cc_final: 0.6590 (m) REVERT: M 220 LEU cc_start: 0.8202 (mt) cc_final: 0.7988 (mt) REVERT: M 227 LEU cc_start: 0.8905 (mt) cc_final: 0.8594 (mp) REVERT: M 240 LYS cc_start: 0.8411 (mttt) cc_final: 0.8006 (mttt) REVERT: M 252 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8433 (Cg_exo) REVERT: M 257 PHE cc_start: 0.8283 (p90) cc_final: 0.8061 (p90) REVERT: M 258 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7957 (mtm-85) REVERT: M 259 LEU cc_start: 0.8660 (tp) cc_final: 0.8353 (tp) REVERT: M 298 LYS cc_start: 0.8303 (tttt) cc_final: 0.7952 (tttt) REVERT: M 299 GLN cc_start: 0.7408 (mt0) cc_final: 0.5853 (mt0) REVERT: M 300 ASN cc_start: 0.8434 (p0) cc_final: 0.8056 (p0) REVERT: M 414 PHE cc_start: 0.7647 (t80) cc_final: 0.7103 (t80) REVERT: C 22 MET cc_start: 0.7581 (ttm) cc_final: 0.6876 (ttm) REVERT: C 39 LEU cc_start: 0.8509 (mt) cc_final: 0.8248 (mt) REVERT: C 45 THR cc_start: 0.8728 (p) cc_final: 0.8421 (t) REVERT: C 64 THR cc_start: 0.7108 (m) cc_final: 0.6575 (t) REVERT: C 68 VAL cc_start: 0.8500 (t) cc_final: 0.8107 (p) REVERT: C 81 TYR cc_start: 0.7067 (m-80) cc_final: 0.6220 (m-80) REVERT: C 82 PHE cc_start: 0.8163 (m-10) cc_final: 0.7730 (m-80) REVERT: C 84 ASN cc_start: 0.8272 (t0) cc_final: 0.7804 (t0) REVERT: C 91 VAL cc_start: 0.8704 (t) cc_final: 0.8430 (p) REVERT: C 121 LEU cc_start: 0.7884 (tp) cc_final: 0.7679 (tp) REVERT: C 128 GLN cc_start: 0.7670 (mm-40) cc_final: 0.6734 (mm-40) REVERT: C 143 LEU cc_start: 0.8830 (mt) cc_final: 0.8580 (mt) REVERT: C 150 HIS cc_start: 0.8771 (m-70) cc_final: 0.8538 (m90) REVERT: C 159 CYS cc_start: 0.7969 (t) cc_final: 0.7390 (t) REVERT: C 170 LEU cc_start: 0.8351 (mt) cc_final: 0.8101 (tp) REVERT: C 172 TRP cc_start: 0.8398 (t60) cc_final: 0.7347 (t60) REVERT: b 43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7952 (tttm) REVERT: b 49 GLN cc_start: 0.8647 (mt0) cc_final: 0.8381 (pt0) REVERT: b 50 MET cc_start: 0.8584 (mtm) cc_final: 0.8236 (mpp) REVERT: b 51 LEU cc_start: 0.8612 (mt) cc_final: 0.8278 (mt) REVERT: b 52 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7712 (mm-30) REVERT: b 54 ASN cc_start: 0.7883 (p0) cc_final: 0.7409 (t0) REVERT: b 55 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7971 (mtmt) REVERT: b 59 LYS cc_start: 0.8483 (mttm) cc_final: 0.8216 (mttp) REVERT: b 63 MET cc_start: 0.8454 (mmm) cc_final: 0.8045 (mmm) REVERT: b 72 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8451 (mtmt) REVERT: b 97 LEU cc_start: 0.8942 (mt) cc_final: 0.8424 (mm) REVERT: b 101 TYR cc_start: 0.8576 (t80) cc_final: 0.8361 (t80) REVERT: b 119 THR cc_start: 0.8445 (t) cc_final: 0.8070 (m) REVERT: b 121 GLN cc_start: 0.8155 (tt0) cc_final: 0.7882 (mt0) REVERT: b 131 ILE cc_start: 0.8647 (mt) cc_final: 0.8429 (mm) REVERT: b 132 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8092 (ttm170) REVERT: b 141 SER cc_start: 0.8552 (m) cc_final: 0.8149 (t) REVERT: b 165 TYR cc_start: 0.8641 (t80) cc_final: 0.8400 (t80) REVERT: b 169 ASN cc_start: 0.8742 (m-40) cc_final: 0.8347 (t0) REVERT: b 175 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8158 (tm-30) REVERT: b 181 ASP cc_start: 0.7968 (t0) cc_final: 0.7439 (t0) REVERT: b 183 GLU cc_start: 0.8809 (mm-30) cc_final: 0.7736 (tm-30) REVERT: b 185 LYS cc_start: 0.7920 (tttt) cc_final: 0.7614 (ttpp) REVERT: b 190 GLU cc_start: 0.8019 (tt0) cc_final: 0.7112 (tt0) REVERT: b 191 VAL cc_start: 0.8948 (t) cc_final: 0.8220 (t) REVERT: b 193 GLU cc_start: 0.8400 (tt0) cc_final: 0.8182 (tt0) REVERT: b 194 LYS cc_start: 0.9013 (mttt) cc_final: 0.8439 (mttt) REVERT: b 195 LEU cc_start: 0.8780 (mt) cc_final: 0.8468 (mt) REVERT: b 196 LEU cc_start: 0.8508 (mt) cc_final: 0.8054 (tp) REVERT: b 215 CYS cc_start: 0.7862 (t) cc_final: 0.7008 (t) REVERT: b 226 TYR cc_start: 0.7891 (t80) cc_final: 0.7583 (t80) REVERT: b 237 GLU cc_start: 0.7553 (tt0) cc_final: 0.7332 (tt0) REVERT: b 241 GLN cc_start: 0.8367 (mt0) cc_final: 0.7574 (mt0) REVERT: b 244 ILE cc_start: 0.9182 (mt) cc_final: 0.8751 (tp) REVERT: b 246 HIS cc_start: 0.8403 (m-70) cc_final: 0.7945 (m-70) REVERT: b 247 MET cc_start: 0.7488 (tmm) cc_final: 0.7098 (tmm) REVERT: b 298 ARG cc_start: 0.8425 (mmm160) cc_final: 0.7682 (mpt180) REVERT: b 300 LEU cc_start: 0.8681 (tp) cc_final: 0.8459 (tp) REVERT: b 303 ASN cc_start: 0.8493 (m-40) cc_final: 0.7793 (t0) REVERT: b 305 LYS cc_start: 0.8984 (tttt) cc_final: 0.8735 (ttpp) REVERT: b 307 LEU cc_start: 0.8962 (mt) cc_final: 0.8726 (mm) REVERT: b 308 LEU cc_start: 0.8483 (mt) cc_final: 0.8205 (mm) REVERT: b 311 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7736 (ptt-90) REVERT: b 317 MET cc_start: 0.8587 (tpp) cc_final: 0.8202 (tpt) REVERT: b 321 GLN cc_start: 0.7724 (tt0) cc_final: 0.7485 (tt0) REVERT: b 326 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (mm) REVERT: b 355 GLN cc_start: 0.8464 (mt0) cc_final: 0.8242 (mt0) REVERT: b 359 THR cc_start: 0.7643 (m) cc_final: 0.7411 (p) REVERT: b 411 THR cc_start: 0.8470 (m) cc_final: 0.8097 (p) REVERT: b 417 ASP cc_start: 0.7850 (t0) cc_final: 0.7535 (m-30) REVERT: b 640 PRO cc_start: 0.8598 (Cg_exo) cc_final: 0.8240 (Cg_endo) REVERT: m 1 MET cc_start: 0.6831 (mtt) cc_final: 0.6378 (mtt) REVERT: m 29 CYS cc_start: 0.8387 (m) cc_final: 0.7948 (t) REVERT: m 33 PHE cc_start: 0.8540 (m-80) cc_final: 0.8196 (m-80) REVERT: m 36 GLN cc_start: 0.8554 (tp40) cc_final: 0.8333 (tp40) REVERT: m 43 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7382 (mt-10) REVERT: m 53 HIS cc_start: 0.8043 (m-70) cc_final: 0.7839 (m-70) REVERT: m 55 TYR cc_start: 0.8044 (m-80) cc_final: 0.7828 (m-80) REVERT: m 64 LEU cc_start: 0.8638 (tp) cc_final: 0.8411 (tp) REVERT: m 77 LEU cc_start: 0.8732 (mt) cc_final: 0.8415 (mp) REVERT: m 78 PHE cc_start: 0.9036 (t80) cc_final: 0.8817 (t80) REVERT: m 81 GLU cc_start: 0.7411 (tp30) cc_final: 0.6606 (tp30) REVERT: m 108 ILE cc_start: 0.8758 (mt) cc_final: 0.8530 (mm) REVERT: m 115 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7686 (tp30) REVERT: m 116 MET cc_start: 0.7588 (mtm) cc_final: 0.6964 (mtm) REVERT: m 119 ASN cc_start: 0.8344 (t0) cc_final: 0.7968 (t0) REVERT: m 126 GLU cc_start: 0.8075 (tp30) cc_final: 0.7758 (tp30) REVERT: m 134 ILE cc_start: 0.8057 (mt) cc_final: 0.7473 (mt) REVERT: m 157 LEU cc_start: 0.8414 (mt) cc_final: 0.8032 (pp) REVERT: m 158 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: m 173 LYS cc_start: 0.7504 (tttt) cc_final: 0.7230 (tttt) REVERT: m 181 PHE cc_start: 0.8079 (m-80) cc_final: 0.7751 (m-80) REVERT: m 182 ASP cc_start: 0.6706 (m-30) cc_final: 0.6303 (m-30) REVERT: m 203 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7091 (mm-40) REVERT: m 209 CYS cc_start: 0.7581 (t) cc_final: 0.6507 (m) REVERT: m 234 HIS cc_start: 0.7295 (t-90) cc_final: 0.6932 (t-90) REVERT: m 240 LYS cc_start: 0.8505 (mttt) cc_final: 0.8059 (mtpp) REVERT: m 257 PHE cc_start: 0.8217 (p90) cc_final: 0.7885 (p90) REVERT: m 258 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7960 (mtm-85) REVERT: m 259 LEU cc_start: 0.8606 (tp) cc_final: 0.8293 (tp) REVERT: m 272 ILE cc_start: 0.6702 (mm) cc_final: 0.5993 (mm) REVERT: m 274 VAL cc_start: 0.7682 (t) cc_final: 0.7462 (p) REVERT: m 298 LYS cc_start: 0.8417 (tttt) cc_final: 0.8147 (tttt) REVERT: m 300 ASN cc_start: 0.8585 (p0) cc_final: 0.8215 (p0) REVERT: m 373 LEU cc_start: 0.6589 (tp) cc_final: 0.6261 (tt) REVERT: m 377 PHE cc_start: 0.8233 (p90) cc_final: 0.7649 (p90) REVERT: m 414 PHE cc_start: 0.7743 (t80) cc_final: 0.7007 (t80) REVERT: c 18 MET cc_start: 0.6253 (mmt) cc_final: 0.6033 (mmt) REVERT: c 21 LEU cc_start: 0.8527 (tp) cc_final: 0.8263 (tp) REVERT: c 39 LEU cc_start: 0.8462 (mt) cc_final: 0.8247 (mt) REVERT: c 45 THR cc_start: 0.8798 (p) cc_final: 0.8510 (t) REVERT: c 64 THR cc_start: 0.7127 (m) cc_final: 0.6578 (t) REVERT: c 82 PHE cc_start: 0.8259 (m-10) cc_final: 0.8036 (m-80) REVERT: c 84 ASN cc_start: 0.8359 (t0) cc_final: 0.6710 (t0) REVERT: c 91 VAL cc_start: 0.8581 (t) cc_final: 0.8316 (t) REVERT: c 110 MET cc_start: 0.8495 (mmm) cc_final: 0.7974 (mmm) REVERT: c 118 ASP cc_start: 0.8165 (m-30) cc_final: 0.7958 (t0) REVERT: c 168 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 8 outliers final: 4 residues processed: 834 average time/residue: 0.3289 time to fit residues: 390.7037 Evaluate side-chains 791 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 785 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0060 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN B 309 GLN B 321 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 309 GLN b 321 GLN m 54 HIS m 161 GLN ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 380 GLN ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115024 restraints weight = 31067.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119383 restraints weight = 16565.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122380 restraints weight = 10196.881| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16108 Z= 0.241 Angle : 0.663 7.954 21822 Z= 0.357 Chirality : 0.047 0.171 2524 Planarity : 0.005 0.058 2752 Dihedral : 11.395 177.967 2154 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.17 % Allowed : 1.36 % Favored : 98.47 % 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: 1.09 (0.20), residues: 1954 helix: 0.74 (0.18), residues: 818 sheet: 0.02 (0.27), residues: 360 loop : 1.40 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 242 HIS 0.017 0.001 HIS m 278 PHE 0.015 0.002 PHE B 211 TYR 0.022 0.003 TYR M 180 ARG 0.005 0.001 ARG c 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 803 time to evaluate : 1.717 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 43 LYS cc_start: 0.8295 (mttt) cc_final: 0.7623 (mmmt) REVERT: B 45 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 48 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8513 (mtmm) REVERT: B 50 MET cc_start: 0.8651 (mtm) cc_final: 0.8269 (mtm) REVERT: B 54 ASN cc_start: 0.7595 (p0) cc_final: 0.7024 (t0) REVERT: B 55 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7914 (mtpt) REVERT: B 63 MET cc_start: 0.8514 (mmm) cc_final: 0.7763 (mmm) REVERT: B 64 LYS cc_start: 0.8944 (mttt) cc_final: 0.8440 (mtpp) REVERT: B 72 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8452 (mtmt) REVERT: B 74 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8373 (mmtt) REVERT: B 79 LEU cc_start: 0.8496 (mt) cc_final: 0.8280 (mt) REVERT: B 83 VAL cc_start: 0.8394 (t) cc_final: 0.7997 (t) REVERT: B 85 LYS cc_start: 0.8678 (mttt) cc_final: 0.8368 (mttt) REVERT: B 90 LYS cc_start: 0.8245 (mttt) cc_final: 0.7868 (mttt) REVERT: B 101 TYR cc_start: 0.8528 (t80) cc_final: 0.8177 (t80) REVERT: B 104 ARG cc_start: 0.8618 (tpt90) cc_final: 0.8372 (tpt90) REVERT: B 125 LYS cc_start: 0.8755 (mttt) cc_final: 0.8356 (mtpp) REVERT: B 132 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8116 (ttm170) REVERT: B 139 LEU cc_start: 0.8412 (tp) cc_final: 0.8182 (tt) REVERT: B 141 SER cc_start: 0.8425 (m) cc_final: 0.8174 (m) REVERT: B 142 ILE cc_start: 0.8958 (mm) cc_final: 0.8615 (mp) REVERT: B 151 MET cc_start: 0.7958 (mtp) cc_final: 0.7663 (mtp) REVERT: B 166 VAL cc_start: 0.8656 (t) cc_final: 0.8427 (p) REVERT: B 190 GLU cc_start: 0.8213 (tt0) cc_final: 0.7998 (tt0) REVERT: B 191 VAL cc_start: 0.9033 (t) cc_final: 0.8792 (p) REVERT: B 193 GLU cc_start: 0.8428 (tt0) cc_final: 0.8181 (tt0) REVERT: B 196 LEU cc_start: 0.8547 (mt) cc_final: 0.8263 (tp) REVERT: B 202 LEU cc_start: 0.7771 (mm) cc_final: 0.7332 (tp) REVERT: B 207 VAL cc_start: 0.8942 (t) cc_final: 0.8620 (p) REVERT: B 215 CYS cc_start: 0.8175 (t) cc_final: 0.7962 (t) REVERT: B 244 ILE cc_start: 0.9060 (mt) cc_final: 0.8717 (tp) REVERT: B 246 HIS cc_start: 0.8330 (m-70) cc_final: 0.8128 (m-70) REVERT: B 247 MET cc_start: 0.7505 (tmm) cc_final: 0.7098 (tmm) REVERT: B 298 ARG cc_start: 0.8516 (mmm160) cc_final: 0.7786 (mpt180) REVERT: B 305 LYS cc_start: 0.8756 (tttt) cc_final: 0.8274 (ttpp) REVERT: B 308 LEU cc_start: 0.8531 (mt) cc_final: 0.8267 (mm) REVERT: B 311 ARG cc_start: 0.8403 (ptt180) cc_final: 0.7755 (ptt-90) REVERT: B 321 GLN cc_start: 0.7949 (tt0) cc_final: 0.7671 (tt0) REVERT: B 322 LEU cc_start: 0.8435 (tt) cc_final: 0.8200 (tt) REVERT: B 324 TRP cc_start: 0.8785 (t-100) cc_final: 0.8521 (t-100) REVERT: B 326 ILE cc_start: 0.8006 (mm) cc_final: 0.7701 (mm) REVERT: B 341 ARG cc_start: 0.8739 (ptt90) cc_final: 0.8324 (ptm-80) REVERT: B 349 VAL cc_start: 0.8302 (t) cc_final: 0.8095 (t) REVERT: B 387 THR cc_start: 0.8465 (m) cc_final: 0.8180 (m) REVERT: B 388 LEU cc_start: 0.8628 (mt) cc_final: 0.8397 (mm) REVERT: B 391 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 417 ASP cc_start: 0.8064 (t0) cc_final: 0.7822 (t0) REVERT: M 1 MET cc_start: 0.6771 (mtt) cc_final: 0.6462 (mtt) REVERT: M 17 GLU cc_start: 0.7751 (pt0) cc_final: 0.7473 (pt0) REVERT: M 21 LYS cc_start: 0.8125 (mttt) cc_final: 0.7279 (mtpp) REVERT: M 30 ASP cc_start: 0.8299 (m-30) cc_final: 0.8075 (t0) REVERT: M 43 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7458 (mt-10) REVERT: M 64 LEU cc_start: 0.8393 (tp) cc_final: 0.8187 (tp) REVERT: M 67 VAL cc_start: 0.8208 (t) cc_final: 0.7889 (m) REVERT: M 71 GLN cc_start: 0.8369 (tp40) cc_final: 0.8078 (tp-100) REVERT: M 74 VAL cc_start: 0.8881 (t) cc_final: 0.8457 (p) REVERT: M 78 PHE cc_start: 0.8874 (t80) cc_final: 0.8553 (t80) REVERT: M 89 THR cc_start: 0.8889 (m) cc_final: 0.8426 (p) REVERT: M 92 ASP cc_start: 0.7753 (t0) cc_final: 0.7421 (t0) REVERT: M 96 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6609 (tm-30) REVERT: M 115 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8014 (tp30) REVERT: M 116 MET cc_start: 0.7828 (mtm) cc_final: 0.7337 (mtm) REVERT: M 119 ASN cc_start: 0.8393 (t0) cc_final: 0.7784 (t0) REVERT: M 121 PHE cc_start: 0.7657 (t80) cc_final: 0.7204 (t80) REVERT: M 126 GLU cc_start: 0.8134 (tp30) cc_final: 0.7475 (tp30) REVERT: M 128 ASN cc_start: 0.8640 (m-40) cc_final: 0.7883 (m110) REVERT: M 131 LYS cc_start: 0.8567 (mttp) cc_final: 0.8061 (mttt) REVERT: M 134 ILE cc_start: 0.8408 (mt) cc_final: 0.7922 (mt) REVERT: M 135 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8347 (mmtt) REVERT: M 153 VAL cc_start: 0.7890 (t) cc_final: 0.7523 (m) REVERT: M 157 LEU cc_start: 0.8342 (mt) cc_final: 0.8046 (pp) REVERT: M 159 THR cc_start: 0.8069 (m) cc_final: 0.7769 (t) REVERT: M 173 LYS cc_start: 0.7757 (tttt) cc_final: 0.7438 (tttt) REVERT: M 183 VAL cc_start: 0.8336 (t) cc_final: 0.8072 (p) REVERT: M 209 CYS cc_start: 0.7550 (t) cc_final: 0.7122 (t) REVERT: M 227 LEU cc_start: 0.8998 (mt) cc_final: 0.8631 (mp) REVERT: M 240 LYS cc_start: 0.8489 (mttt) cc_final: 0.8141 (mttt) REVERT: M 242 TRP cc_start: 0.7156 (t-100) cc_final: 0.6898 (t-100) REVERT: M 257 PHE cc_start: 0.8342 (p90) cc_final: 0.8054 (p90) REVERT: M 258 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7954 (mtm-85) REVERT: M 262 TYR cc_start: 0.8393 (p90) cc_final: 0.7984 (p90) REVERT: M 298 LYS cc_start: 0.8882 (tttt) cc_final: 0.8485 (tttt) REVERT: M 300 ASN cc_start: 0.8909 (p0) cc_final: 0.8652 (p0) REVERT: M 345 LYS cc_start: 0.7243 (ptmm) cc_final: 0.6333 (mtpp) REVERT: M 377 PHE cc_start: 0.7885 (p90) cc_final: 0.7453 (p90) REVERT: M 393 ASP cc_start: 0.7992 (t0) cc_final: 0.7686 (t0) REVERT: M 402 PHE cc_start: 0.7564 (m-80) cc_final: 0.7148 (m-80) REVERT: M 407 TYR cc_start: 0.8577 (m-80) cc_final: 0.8242 (m-80) REVERT: M 414 PHE cc_start: 0.7729 (t80) cc_final: 0.7139 (t80) REVERT: C 21 LEU cc_start: 0.8399 (tp) cc_final: 0.8116 (tp) REVERT: C 51 PHE cc_start: 0.8124 (p90) cc_final: 0.7877 (p90) REVERT: C 53 VAL cc_start: 0.8255 (p) cc_final: 0.8041 (t) REVERT: C 58 TYR cc_start: 0.7904 (t80) cc_final: 0.7373 (t80) REVERT: C 64 THR cc_start: 0.6795 (m) cc_final: 0.6577 (t) REVERT: C 78 TRP cc_start: 0.8163 (m-10) cc_final: 0.7489 (m-10) REVERT: C 81 TYR cc_start: 0.7287 (m-80) cc_final: 0.6756 (m-80) REVERT: C 84 ASN cc_start: 0.8391 (t0) cc_final: 0.7747 (t0) REVERT: C 110 MET cc_start: 0.8385 (mmm) cc_final: 0.7974 (mmm) REVERT: C 128 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6548 (mm-40) REVERT: C 143 LEU cc_start: 0.8856 (mt) cc_final: 0.8642 (mt) REVERT: C 145 LEU cc_start: 0.8229 (mt) cc_final: 0.7971 (mt) REVERT: C 153 TRP cc_start: 0.8509 (p-90) cc_final: 0.8000 (p-90) REVERT: C 159 CYS cc_start: 0.8303 (t) cc_final: 0.7880 (t) REVERT: C 167 TYR cc_start: 0.7851 (m-10) cc_final: 0.7134 (m-80) REVERT: C 168 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7883 (mt-10) REVERT: C 171 ASP cc_start: 0.8324 (m-30) cc_final: 0.7982 (m-30) REVERT: C 172 TRP cc_start: 0.8237 (t60) cc_final: 0.7357 (t60) REVERT: C 176 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7370 (mm-40) REVERT: b 43 LYS cc_start: 0.8185 (mttt) cc_final: 0.7795 (tttp) REVERT: b 50 MET cc_start: 0.8614 (mtm) cc_final: 0.8267 (mpp) REVERT: b 63 MET cc_start: 0.8518 (mmm) cc_final: 0.7749 (mmm) REVERT: b 79 LEU cc_start: 0.8552 (mt) cc_final: 0.8245 (mt) REVERT: b 83 VAL cc_start: 0.8299 (t) cc_final: 0.8011 (t) REVERT: b 85 LYS cc_start: 0.8670 (mttt) cc_final: 0.8463 (mttt) REVERT: b 90 LYS cc_start: 0.8143 (mttm) cc_final: 0.7891 (ttmm) REVERT: b 101 TYR cc_start: 0.8564 (t80) cc_final: 0.8354 (t80) REVERT: b 112 LEU cc_start: 0.8088 (mp) cc_final: 0.7711 (mp) REVERT: b 131 ILE cc_start: 0.8563 (mt) cc_final: 0.8350 (mm) REVERT: b 132 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8202 (ttm170) REVERT: b 139 LEU cc_start: 0.8338 (tp) cc_final: 0.8110 (tt) REVERT: b 141 SER cc_start: 0.8468 (m) cc_final: 0.7946 (t) REVERT: b 142 ILE cc_start: 0.8995 (mm) cc_final: 0.8588 (mp) REVERT: b 151 MET cc_start: 0.7828 (mtp) cc_final: 0.7458 (mtp) REVERT: b 166 VAL cc_start: 0.8695 (t) cc_final: 0.8459 (p) REVERT: b 181 ASP cc_start: 0.8113 (t0) cc_final: 0.7677 (t0) REVERT: b 191 VAL cc_start: 0.8993 (t) cc_final: 0.8736 (p) REVERT: b 195 LEU cc_start: 0.8999 (mt) cc_final: 0.8673 (mt) REVERT: b 196 LEU cc_start: 0.8631 (mt) cc_final: 0.8249 (tp) REVERT: b 202 LEU cc_start: 0.7925 (mm) cc_final: 0.7468 (tt) REVERT: b 207 VAL cc_start: 0.8942 (t) cc_final: 0.8526 (p) REVERT: b 212 GLU cc_start: 0.8332 (tp30) cc_final: 0.8121 (tp30) REVERT: b 215 CYS cc_start: 0.8304 (t) cc_final: 0.8085 (t) REVERT: b 228 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8027 (ttpt) REVERT: b 244 ILE cc_start: 0.9118 (mt) cc_final: 0.8725 (tp) REVERT: b 247 MET cc_start: 0.7626 (tmm) cc_final: 0.6668 (tmm) REVERT: b 298 ARG cc_start: 0.8654 (mmm160) cc_final: 0.7472 (mpt180) REVERT: b 305 LYS cc_start: 0.8737 (tttt) cc_final: 0.8426 (ttpp) REVERT: b 307 LEU cc_start: 0.8923 (mt) cc_final: 0.8667 (mm) REVERT: b 308 LEU cc_start: 0.8636 (mt) cc_final: 0.8308 (mm) REVERT: b 311 ARG cc_start: 0.8387 (ptt180) cc_final: 0.7776 (ptt-90) REVERT: b 317 MET cc_start: 0.8776 (tpp) cc_final: 0.8497 (tpt) REVERT: b 321 GLN cc_start: 0.7913 (tt0) cc_final: 0.7537 (tt0) REVERT: b 322 LEU cc_start: 0.8549 (tt) cc_final: 0.8272 (tt) REVERT: b 326 ILE cc_start: 0.8120 (mm) cc_final: 0.7817 (mm) REVERT: b 341 ARG cc_start: 0.8736 (ptt90) cc_final: 0.7867 (ttp80) REVERT: b 352 ILE cc_start: 0.8613 (mm) cc_final: 0.8397 (mm) REVERT: b 417 ASP cc_start: 0.7771 (t0) cc_final: 0.7343 (t0) REVERT: b 645 ASP cc_start: 0.7839 (t0) cc_final: 0.7119 (p0) REVERT: m 1 MET cc_start: 0.6909 (mtt) cc_final: 0.6355 (mtt) REVERT: m 14 ILE cc_start: 0.8021 (mt) cc_final: 0.7729 (mt) REVERT: m 17 GLU cc_start: 0.7715 (pt0) cc_final: 0.7492 (pt0) REVERT: m 24 VAL cc_start: 0.8609 (t) cc_final: 0.8312 (p) REVERT: m 29 CYS cc_start: 0.8492 (m) cc_final: 0.7938 (t) REVERT: m 33 PHE cc_start: 0.8654 (m-80) cc_final: 0.8231 (m-80) REVERT: m 36 GLN cc_start: 0.8503 (tp40) cc_final: 0.8086 (tp40) REVERT: m 43 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7342 (mt-10) REVERT: m 53 HIS cc_start: 0.8226 (m-70) cc_final: 0.7801 (m170) REVERT: m 60 TYR cc_start: 0.7993 (t80) cc_final: 0.7750 (t80) REVERT: m 64 LEU cc_start: 0.8357 (tp) cc_final: 0.8142 (tp) REVERT: m 71 GLN cc_start: 0.8395 (tp40) cc_final: 0.7722 (tp40) REVERT: m 78 PHE cc_start: 0.8839 (t80) cc_final: 0.8537 (t80) REVERT: m 81 GLU cc_start: 0.7623 (tp30) cc_final: 0.7284 (tp30) REVERT: m 88 ASP cc_start: 0.8594 (m-30) cc_final: 0.8317 (m-30) REVERT: m 89 THR cc_start: 0.8961 (m) cc_final: 0.8739 (m) REVERT: m 92 ASP cc_start: 0.7581 (t70) cc_final: 0.7254 (t70) REVERT: m 103 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7176 (mtmm) REVERT: m 108 ILE cc_start: 0.8801 (mt) cc_final: 0.8399 (mm) REVERT: m 116 MET cc_start: 0.7603 (mtm) cc_final: 0.7014 (mtm) REVERT: m 125 THR cc_start: 0.8547 (m) cc_final: 0.8205 (t) REVERT: m 126 GLU cc_start: 0.8160 (tp30) cc_final: 0.7598 (tp30) REVERT: m 128 ASN cc_start: 0.8626 (m-40) cc_final: 0.7751 (m-40) REVERT: m 134 ILE cc_start: 0.8239 (mt) cc_final: 0.7609 (tp) REVERT: m 140 LEU cc_start: 0.8511 (mt) cc_final: 0.8252 (tt) REVERT: m 141 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7846 (mmt90) REVERT: m 183 VAL cc_start: 0.8327 (t) cc_final: 0.8083 (p) REVERT: m 209 CYS cc_start: 0.7384 (t) cc_final: 0.6318 (m) REVERT: m 220 LEU cc_start: 0.8287 (mm) cc_final: 0.7855 (mm) REVERT: m 234 HIS cc_start: 0.7782 (t-90) cc_final: 0.7335 (t-90) REVERT: m 240 LYS cc_start: 0.8620 (mttt) cc_final: 0.7975 (mmmm) REVERT: m 257 PHE cc_start: 0.8365 (p90) cc_final: 0.8029 (p90) REVERT: m 258 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7993 (mtm-85) REVERT: m 272 ILE cc_start: 0.7565 (mm) cc_final: 0.6868 (mm) REVERT: m 274 VAL cc_start: 0.7951 (t) cc_final: 0.7673 (p) REVERT: m 298 LYS cc_start: 0.8963 (tttt) cc_final: 0.8588 (tttt) REVERT: m 300 ASN cc_start: 0.8992 (p0) cc_final: 0.8764 (p0) REVERT: m 377 PHE cc_start: 0.7748 (p90) cc_final: 0.7390 (p90) REVERT: m 402 PHE cc_start: 0.7585 (m-80) cc_final: 0.6979 (m-80) REVERT: m 414 PHE cc_start: 0.7894 (t80) cc_final: 0.7218 (t80) REVERT: c 18 MET cc_start: 0.6184 (mmt) cc_final: 0.5855 (mmt) REVERT: c 21 LEU cc_start: 0.8443 (tp) cc_final: 0.8212 (tp) REVERT: c 45 THR cc_start: 0.9008 (p) cc_final: 0.8626 (t) REVERT: c 58 TYR cc_start: 0.7930 (t80) cc_final: 0.7189 (t80) REVERT: c 64 THR cc_start: 0.6839 (m) cc_final: 0.6424 (t) REVERT: c 78 TRP cc_start: 0.8200 (m-10) cc_final: 0.7397 (m-10) REVERT: c 84 ASN cc_start: 0.8015 (t0) cc_final: 0.7158 (t0) REVERT: c 86 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6965 (mt0) REVERT: c 110 MET cc_start: 0.8322 (mmm) cc_final: 0.7812 (mmm) REVERT: c 128 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6501 (mm-40) REVERT: c 151 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8056 (ttm-80) REVERT: c 159 CYS cc_start: 0.8384 (t) cc_final: 0.8034 (t) REVERT: c 167 TYR cc_start: 0.7892 (m-10) cc_final: 0.7235 (m-80) REVERT: c 168 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8003 (mt-10) REVERT: c 171 ASP cc_start: 0.8450 (m-30) cc_final: 0.8145 (m-30) outliers start: 3 outliers final: 2 residues processed: 805 average time/residue: 0.3126 time to fit residues: 356.9836 Evaluate side-chains 754 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 752 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 GLN ** m 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 54 HIS ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113134 restraints weight = 31013.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117371 restraints weight = 16733.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120225 restraints weight = 10403.380| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16108 Z= 0.306 Angle : 0.666 8.490 21822 Z= 0.360 Chirality : 0.048 0.181 2524 Planarity : 0.005 0.041 2752 Dihedral : 11.133 177.692 2154 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.17 % Allowed : 2.04 % Favored : 97.79 % 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: 1.05 (0.20), residues: 1954 helix: 0.92 (0.18), residues: 816 sheet: -0.01 (0.27), residues: 370 loop : 1.13 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP c 66 HIS 0.004 0.001 HIS M 54 PHE 0.025 0.002 PHE C 82 TYR 0.024 0.002 TYR M 110 ARG 0.007 0.001 ARG b 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 796 time to evaluate : 1.800 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: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8188 (mttt) cc_final: 0.7630 (tptp) REVERT: B 47 LEU cc_start: 0.8985 (mt) cc_final: 0.8481 (mt) REVERT: B 50 MET cc_start: 0.8620 (mtm) cc_final: 0.8190 (mtm) REVERT: B 51 LEU cc_start: 0.8775 (mt) cc_final: 0.8531 (mt) REVERT: B 52 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 55 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8218 (mtpt) REVERT: B 63 MET cc_start: 0.8504 (mmm) cc_final: 0.7787 (mmm) REVERT: B 66 ILE cc_start: 0.8710 (mm) cc_final: 0.8166 (mm) REVERT: B 72 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8491 (mtmt) REVERT: B 74 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8350 (mmtt) REVERT: B 79 LEU cc_start: 0.8671 (mt) cc_final: 0.8461 (mt) REVERT: B 80 PHE cc_start: 0.8549 (t80) cc_final: 0.7546 (t80) REVERT: B 83 VAL cc_start: 0.8428 (t) cc_final: 0.8219 (t) REVERT: B 84 VAL cc_start: 0.8615 (p) cc_final: 0.8301 (m) REVERT: B 85 LYS cc_start: 0.8620 (mttt) cc_final: 0.8225 (mttt) REVERT: B 90 LYS cc_start: 0.8514 (mttt) cc_final: 0.8216 (mttt) REVERT: B 94 ILE cc_start: 0.8406 (mt) cc_final: 0.8124 (mm) REVERT: B 101 TYR cc_start: 0.8594 (t80) cc_final: 0.8386 (t80) REVERT: B 104 ARG cc_start: 0.8749 (tpt90) cc_final: 0.8363 (tpt90) REVERT: B 112 LEU cc_start: 0.8299 (mp) cc_final: 0.7572 (mp) REVERT: B 125 LYS cc_start: 0.8861 (mttt) cc_final: 0.8365 (mtpp) REVERT: B 132 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8044 (mtm-85) REVERT: B 137 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7565 (mtp-110) REVERT: B 139 LEU cc_start: 0.8571 (tp) cc_final: 0.8370 (tt) REVERT: B 141 SER cc_start: 0.8544 (m) cc_final: 0.8274 (m) REVERT: B 142 ILE cc_start: 0.9032 (mm) cc_final: 0.8799 (mp) REVERT: B 147 ILE cc_start: 0.8594 (pt) cc_final: 0.8371 (pt) REVERT: B 151 MET cc_start: 0.7862 (mtp) cc_final: 0.7470 (mtp) REVERT: B 152 MET cc_start: 0.8187 (tpt) cc_final: 0.7909 (tpt) REVERT: B 172 HIS cc_start: 0.8574 (m170) cc_final: 0.8105 (m-70) REVERT: B 193 GLU cc_start: 0.8384 (tt0) cc_final: 0.8121 (tt0) REVERT: B 196 LEU cc_start: 0.8660 (mt) cc_final: 0.8332 (tp) REVERT: B 199 LYS cc_start: 0.8079 (mptt) cc_final: 0.7874 (mmtm) REVERT: B 202 LEU cc_start: 0.7849 (mm) cc_final: 0.7374 (tp) REVERT: B 207 VAL cc_start: 0.9000 (t) cc_final: 0.8705 (p) REVERT: B 209 MET cc_start: 0.7633 (ttp) cc_final: 0.7355 (ttt) REVERT: B 212 GLU cc_start: 0.8262 (tp30) cc_final: 0.8003 (tp30) REVERT: B 215 CYS cc_start: 0.8327 (t) cc_final: 0.7899 (t) REVERT: B 218 ARG cc_start: 0.8929 (mmm160) cc_final: 0.8638 (mtp-110) REVERT: B 228 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8006 (ttpt) REVERT: B 244 ILE cc_start: 0.9090 (mt) cc_final: 0.8647 (tp) REVERT: B 246 HIS cc_start: 0.8485 (m-70) cc_final: 0.8175 (m-70) REVERT: B 247 MET cc_start: 0.7338 (tmm) cc_final: 0.6052 (tmm) REVERT: B 298 ARG cc_start: 0.8623 (mmm160) cc_final: 0.7779 (mpt180) REVERT: B 305 LYS cc_start: 0.8791 (tttt) cc_final: 0.8325 (ttpp) REVERT: B 308 LEU cc_start: 0.8593 (mt) cc_final: 0.8301 (mm) REVERT: B 311 ARG cc_start: 0.8352 (ptt180) cc_final: 0.7614 (ptt-90) REVERT: B 317 MET cc_start: 0.8696 (tpp) cc_final: 0.8304 (tpp) REVERT: B 321 GLN cc_start: 0.8009 (tt0) cc_final: 0.7456 (tt0) REVERT: B 322 LEU cc_start: 0.8422 (tt) cc_final: 0.8221 (tt) REVERT: B 326 ILE cc_start: 0.8105 (mm) cc_final: 0.7778 (mm) REVERT: B 341 ARG cc_start: 0.8772 (ptt90) cc_final: 0.8309 (ptm-80) REVERT: B 346 ASN cc_start: 0.7055 (p0) cc_final: 0.6848 (p0) REVERT: B 351 TYR cc_start: 0.8029 (t80) cc_final: 0.7380 (t80) REVERT: B 387 THR cc_start: 0.8437 (m) cc_final: 0.8188 (m) REVERT: B 388 LEU cc_start: 0.8743 (mt) cc_final: 0.8455 (mm) REVERT: B 391 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 417 ASP cc_start: 0.8125 (t0) cc_final: 0.7876 (t0) REVERT: B 635 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 640 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8668 (Cg_endo) REVERT: M 21 LYS cc_start: 0.8091 (mttt) cc_final: 0.7576 (mttm) REVERT: M 26 GLN cc_start: 0.8423 (mt0) cc_final: 0.7934 (tp40) REVERT: M 29 CYS cc_start: 0.8646 (t) cc_final: 0.8207 (t) REVERT: M 30 ASP cc_start: 0.8229 (m-30) cc_final: 0.8006 (t0) REVERT: M 43 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7442 (mt-10) REVERT: M 56 LEU cc_start: 0.8535 (mm) cc_final: 0.8304 (mm) REVERT: M 64 LEU cc_start: 0.8507 (tp) cc_final: 0.8306 (tp) REVERT: M 74 VAL cc_start: 0.8941 (t) cc_final: 0.8651 (p) REVERT: M 78 PHE cc_start: 0.8898 (t80) cc_final: 0.8614 (t80) REVERT: M 88 ASP cc_start: 0.8626 (m-30) cc_final: 0.8340 (m-30) REVERT: M 89 THR cc_start: 0.8974 (m) cc_final: 0.8581 (p) REVERT: M 108 ILE cc_start: 0.8836 (mt) cc_final: 0.8622 (mt) REVERT: M 116 MET cc_start: 0.7950 (mtm) cc_final: 0.7699 (mtm) REVERT: M 126 GLU cc_start: 0.8084 (tp30) cc_final: 0.7469 (tp30) REVERT: M 128 ASN cc_start: 0.8330 (m-40) cc_final: 0.7910 (m-40) REVERT: M 131 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8087 (mttp) REVERT: M 134 ILE cc_start: 0.8230 (mt) cc_final: 0.7760 (mt) REVERT: M 135 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8347 (mmtt) REVERT: M 157 LEU cc_start: 0.8475 (mt) cc_final: 0.8171 (pp) REVERT: M 159 THR cc_start: 0.8225 (m) cc_final: 0.7846 (t) REVERT: M 161 GLN cc_start: 0.8346 (tp40) cc_final: 0.8014 (tp-100) REVERT: M 173 LYS cc_start: 0.8159 (tttt) cc_final: 0.7814 (tttt) REVERT: M 183 VAL cc_start: 0.8533 (t) cc_final: 0.8257 (p) REVERT: M 203 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6764 (mm-40) REVERT: M 220 LEU cc_start: 0.8375 (mm) cc_final: 0.8040 (mm) REVERT: M 227 LEU cc_start: 0.8962 (mt) cc_final: 0.8484 (mp) REVERT: M 234 HIS cc_start: 0.7946 (t-90) cc_final: 0.7702 (t-90) REVERT: M 240 LYS cc_start: 0.8550 (mttt) cc_final: 0.8056 (mttt) REVERT: M 242 TRP cc_start: 0.7424 (t-100) cc_final: 0.7077 (t-100) REVERT: M 245 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6819 (mm-30) REVERT: M 251 ILE cc_start: 0.8628 (mm) cc_final: 0.8400 (mm) REVERT: M 257 PHE cc_start: 0.8422 (p90) cc_final: 0.8064 (p90) REVERT: M 258 ARG cc_start: 0.8305 (mtm180) cc_final: 0.8032 (mtm-85) REVERT: M 262 TYR cc_start: 0.8430 (p90) cc_final: 0.7973 (p90) REVERT: M 298 LYS cc_start: 0.8986 (tttt) cc_final: 0.8525 (tttt) REVERT: M 299 GLN cc_start: 0.8167 (mt0) cc_final: 0.6681 (mt0) REVERT: M 312 VAL cc_start: 0.6212 (OUTLIER) cc_final: 0.5706 (m) REVERT: M 377 PHE cc_start: 0.7999 (p90) cc_final: 0.7492 (p90) REVERT: M 393 ASP cc_start: 0.8172 (t0) cc_final: 0.7757 (t0) REVERT: M 402 PHE cc_start: 0.7762 (m-80) cc_final: 0.7254 (m-80) REVERT: M 414 PHE cc_start: 0.7778 (t80) cc_final: 0.7241 (t80) REVERT: C 23 VAL cc_start: 0.8824 (m) cc_final: 0.8388 (m) REVERT: C 37 LEU cc_start: 0.8923 (mt) cc_final: 0.8678 (mt) REVERT: C 51 PHE cc_start: 0.8015 (p90) cc_final: 0.7804 (p90) REVERT: C 58 TYR cc_start: 0.8085 (t80) cc_final: 0.7661 (t80) REVERT: C 64 THR cc_start: 0.6825 (m) cc_final: 0.6527 (t) REVERT: C 68 VAL cc_start: 0.8308 (t) cc_final: 0.8036 (p) REVERT: C 78 TRP cc_start: 0.8215 (m-10) cc_final: 0.7730 (m-10) REVERT: C 84 ASN cc_start: 0.8478 (t0) cc_final: 0.7785 (t0) REVERT: C 86 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7228 (mt0) REVERT: C 145 LEU cc_start: 0.8328 (mt) cc_final: 0.8061 (mt) REVERT: C 153 TRP cc_start: 0.8626 (p-90) cc_final: 0.8390 (p-90) REVERT: C 167 TYR cc_start: 0.8029 (m-10) cc_final: 0.7302 (m-10) REVERT: C 168 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 171 ASP cc_start: 0.8346 (m-30) cc_final: 0.7982 (m-30) REVERT: b 43 LYS cc_start: 0.8244 (mttt) cc_final: 0.7813 (tttp) REVERT: b 47 LEU cc_start: 0.9024 (mt) cc_final: 0.8707 (mt) REVERT: b 50 MET cc_start: 0.8604 (mtm) cc_final: 0.8320 (mtm) REVERT: b 51 LEU cc_start: 0.8820 (mt) cc_final: 0.8619 (mt) REVERT: b 54 ASN cc_start: 0.7684 (t0) cc_final: 0.7170 (t0) REVERT: b 63 MET cc_start: 0.8506 (mmm) cc_final: 0.7626 (mmm) REVERT: b 72 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8360 (mtmt) REVERT: b 74 LYS cc_start: 0.8530 (tppt) cc_final: 0.8233 (mmtp) REVERT: b 80 PHE cc_start: 0.8588 (t80) cc_final: 0.8052 (t80) REVERT: b 83 VAL cc_start: 0.8185 (t) cc_final: 0.7888 (t) REVERT: b 85 LYS cc_start: 0.8616 (mttt) cc_final: 0.8314 (mttt) REVERT: b 98 VAL cc_start: 0.8883 (t) cc_final: 0.8345 (t) REVERT: b 112 LEU cc_start: 0.8162 (mp) cc_final: 0.7363 (mp) REVERT: b 121 GLN cc_start: 0.8173 (tt0) cc_final: 0.7950 (mt0) REVERT: b 131 ILE cc_start: 0.8564 (mt) cc_final: 0.8360 (mm) REVERT: b 132 ARG cc_start: 0.8475 (mtt180) cc_final: 0.8075 (ttm170) REVERT: b 141 SER cc_start: 0.8617 (m) cc_final: 0.8281 (m) REVERT: b 142 ILE cc_start: 0.9065 (mm) cc_final: 0.8711 (mp) REVERT: b 150 ILE cc_start: 0.8208 (mt) cc_final: 0.7987 (mt) REVERT: b 151 MET cc_start: 0.7698 (mtp) cc_final: 0.7253 (mtp) REVERT: b 152 MET cc_start: 0.8138 (tpt) cc_final: 0.7862 (tpt) REVERT: b 162 LEU cc_start: 0.7731 (mt) cc_final: 0.6933 (tp) REVERT: b 175 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8313 (tm-30) REVERT: b 181 ASP cc_start: 0.8282 (t0) cc_final: 0.7852 (t0) REVERT: b 187 MET cc_start: 0.8258 (mtm) cc_final: 0.7938 (mtm) REVERT: b 190 GLU cc_start: 0.8158 (tt0) cc_final: 0.7935 (tt0) REVERT: b 195 LEU cc_start: 0.9112 (mt) cc_final: 0.8775 (mt) REVERT: b 196 LEU cc_start: 0.8758 (mt) cc_final: 0.8314 (tp) REVERT: b 202 LEU cc_start: 0.7898 (mm) cc_final: 0.7505 (tp) REVERT: b 207 VAL cc_start: 0.8940 (t) cc_final: 0.8539 (p) REVERT: b 212 GLU cc_start: 0.8264 (tp30) cc_final: 0.7965 (tp30) REVERT: b 213 GLU cc_start: 0.8326 (tt0) cc_final: 0.7672 (tt0) REVERT: b 215 CYS cc_start: 0.8363 (t) cc_final: 0.7882 (t) REVERT: b 228 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8090 (ttpt) REVERT: b 244 ILE cc_start: 0.9121 (mt) cc_final: 0.8760 (tp) REVERT: b 246 HIS cc_start: 0.8471 (m-70) cc_final: 0.8257 (m-70) REVERT: b 247 MET cc_start: 0.7450 (tmm) cc_final: 0.6925 (tmm) REVERT: b 298 ARG cc_start: 0.8817 (mmm160) cc_final: 0.7405 (mpt180) REVERT: b 305 LYS cc_start: 0.8748 (tttt) cc_final: 0.8527 (tttm) REVERT: b 307 LEU cc_start: 0.8975 (mt) cc_final: 0.8607 (mt) REVERT: b 308 LEU cc_start: 0.8733 (mt) cc_final: 0.8364 (mm) REVERT: b 311 ARG cc_start: 0.8396 (ptt180) cc_final: 0.7728 (ptt-90) REVERT: b 317 MET cc_start: 0.8728 (tpp) cc_final: 0.8464 (tpt) REVERT: b 321 GLN cc_start: 0.8009 (tt0) cc_final: 0.7594 (tt0) REVERT: b 322 LEU cc_start: 0.8504 (tt) cc_final: 0.8260 (tt) REVERT: b 326 ILE cc_start: 0.8135 (mm) cc_final: 0.7922 (mm) REVERT: b 417 ASP cc_start: 0.7896 (t0) cc_final: 0.7351 (t0) REVERT: b 629 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7637 (ttmm) REVERT: b 645 ASP cc_start: 0.7838 (t0) cc_final: 0.7405 (t70) REVERT: m 1 MET cc_start: 0.7036 (mtt) cc_final: 0.6506 (mtt) REVERT: m 14 ILE cc_start: 0.8121 (mt) cc_final: 0.7909 (mt) REVERT: m 17 GLU cc_start: 0.7700 (pt0) cc_final: 0.7331 (pt0) REVERT: m 21 LYS cc_start: 0.8089 (mttt) cc_final: 0.7435 (mttm) REVERT: m 29 CYS cc_start: 0.8403 (m) cc_final: 0.8090 (t) REVERT: m 36 GLN cc_start: 0.8412 (tp40) cc_final: 0.8052 (tp40) REVERT: m 43 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7410 (mt-10) REVERT: m 45 VAL cc_start: 0.8898 (t) cc_final: 0.8666 (t) REVERT: m 71 GLN cc_start: 0.8421 (tp40) cc_final: 0.7719 (tp40) REVERT: m 74 VAL cc_start: 0.9066 (t) cc_final: 0.8682 (p) REVERT: m 77 LEU cc_start: 0.8620 (mt) cc_final: 0.8259 (mt) REVERT: m 78 PHE cc_start: 0.8832 (t80) cc_final: 0.8369 (t80) REVERT: m 81 GLU cc_start: 0.7820 (tp30) cc_final: 0.7450 (tp30) REVERT: m 96 GLU cc_start: 0.6939 (pp20) cc_final: 0.6728 (tm-30) REVERT: m 103 LYS cc_start: 0.7452 (mtmm) cc_final: 0.7154 (mtmm) REVERT: m 108 ILE cc_start: 0.8877 (mt) cc_final: 0.8558 (mm) REVERT: m 111 GLU cc_start: 0.7982 (tt0) cc_final: 0.7773 (tt0) REVERT: m 115 GLU cc_start: 0.8520 (tp30) cc_final: 0.7879 (tp30) REVERT: m 116 MET cc_start: 0.7802 (mtm) cc_final: 0.7498 (mtm) REVERT: m 126 GLU cc_start: 0.8225 (tp30) cc_final: 0.7585 (tp30) REVERT: m 128 ASN cc_start: 0.8357 (m-40) cc_final: 0.7674 (m-40) REVERT: m 134 ILE cc_start: 0.8268 (mt) cc_final: 0.7677 (tp) REVERT: m 140 LEU cc_start: 0.8555 (mt) cc_final: 0.8314 (tt) REVERT: m 141 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7754 (mmt90) REVERT: m 157 LEU cc_start: 0.8466 (mt) cc_final: 0.8141 (pp) REVERT: m 161 GLN cc_start: 0.8394 (tp40) cc_final: 0.8102 (tp-100) REVERT: m 209 CYS cc_start: 0.7463 (t) cc_final: 0.6322 (m) REVERT: m 220 LEU cc_start: 0.8273 (mm) cc_final: 0.7950 (mm) REVERT: m 240 LYS cc_start: 0.8652 (mttt) cc_final: 0.8054 (mmmm) REVERT: m 242 TRP cc_start: 0.7681 (t-100) cc_final: 0.7402 (t-100) REVERT: m 257 PHE cc_start: 0.8485 (p90) cc_final: 0.8144 (p90) REVERT: m 258 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7959 (mtm180) REVERT: m 272 ILE cc_start: 0.7984 (mm) cc_final: 0.6392 (mp) REVERT: m 293 ILE cc_start: 0.7762 (mm) cc_final: 0.7521 (mm) REVERT: m 298 LYS cc_start: 0.9040 (tttt) cc_final: 0.8610 (tttt) REVERT: m 299 GLN cc_start: 0.8405 (mt0) cc_final: 0.6917 (mt0) REVERT: m 373 LEU cc_start: 0.7669 (tt) cc_final: 0.7465 (tt) REVERT: m 377 PHE cc_start: 0.7891 (p90) cc_final: 0.7513 (p90) REVERT: m 378 LYS cc_start: 0.8073 (pttt) cc_final: 0.7697 (ptmm) REVERT: m 400 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8676 (mmtt) REVERT: m 402 PHE cc_start: 0.7545 (m-80) cc_final: 0.7062 (m-80) REVERT: m 406 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8347 (ttmt) REVERT: m 414 PHE cc_start: 0.7894 (t80) cc_final: 0.7496 (t80) REVERT: c 18 MET cc_start: 0.6470 (mmt) cc_final: 0.6138 (mmt) REVERT: c 58 TYR cc_start: 0.8152 (t80) cc_final: 0.7506 (t80) REVERT: c 64 THR cc_start: 0.6810 (m) cc_final: 0.6372 (t) REVERT: c 78 TRP cc_start: 0.8289 (m-10) cc_final: 0.7460 (m-10) REVERT: c 84 ASN cc_start: 0.8307 (t0) cc_final: 0.7691 (t0) REVERT: c 110 MET cc_start: 0.8482 (mmm) cc_final: 0.8009 (mmm) REVERT: c 115 GLU cc_start: 0.7796 (tt0) cc_final: 0.7513 (tt0) REVERT: c 145 LEU cc_start: 0.8399 (mt) cc_final: 0.8087 (mt) REVERT: c 153 TRP cc_start: 0.8691 (p-90) cc_final: 0.8312 (p-90) REVERT: c 159 CYS cc_start: 0.8465 (t) cc_final: 0.8211 (t) REVERT: c 167 TYR cc_start: 0.8089 (m-10) cc_final: 0.7401 (m-10) REVERT: c 168 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7773 (mt-10) REVERT: c 171 ASP cc_start: 0.8411 (m-30) cc_final: 0.8050 (m-30) REVERT: c 178 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7641 (ttm170) outliers start: 3 outliers final: 0 residues processed: 797 average time/residue: 0.3386 time to fit residues: 386.4255 Evaluate side-chains 751 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 750 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 83 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 60 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN M 36 GLN M 54 HIS b 355 GLN m 26 GLN m 54 HIS ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN y 411 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115718 restraints weight = 30869.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120007 restraints weight = 16662.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122981 restraints weight = 10404.199| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16108 Z= 0.184 Angle : 0.586 9.944 21822 Z= 0.308 Chirality : 0.045 0.173 2524 Planarity : 0.004 0.047 2752 Dihedral : 10.764 173.044 2154 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.41 % 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: 1.21 (0.20), residues: 1954 helix: 1.10 (0.18), residues: 818 sheet: 0.10 (0.27), residues: 370 loop : 1.11 (0.25), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 172 HIS 0.003 0.001 HIS b 297 PHE 0.022 0.002 PHE m 121 TYR 0.024 0.002 TYR M 110 ARG 0.006 0.000 ARG B 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 782 time to evaluate : 1.672 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: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8246 (mttt) cc_final: 0.7599 (mmmt) REVERT: B 47 LEU cc_start: 0.9000 (mt) cc_final: 0.8518 (mt) REVERT: B 50 MET cc_start: 0.8655 (mtm) cc_final: 0.8171 (mtm) REVERT: B 51 LEU cc_start: 0.8747 (mt) cc_final: 0.8429 (mt) REVERT: B 52 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 63 MET cc_start: 0.8575 (mmm) cc_final: 0.7777 (mmm) REVERT: B 66 ILE cc_start: 0.8641 (mm) cc_final: 0.8277 (mm) REVERT: B 72 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8506 (mtpt) REVERT: B 74 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8404 (mmtt) REVERT: B 80 PHE cc_start: 0.8486 (t80) cc_final: 0.7696 (t80) REVERT: B 83 VAL cc_start: 0.8383 (t) cc_final: 0.8140 (t) REVERT: B 84 VAL cc_start: 0.8593 (p) cc_final: 0.8286 (m) REVERT: B 85 LYS cc_start: 0.8607 (mttt) cc_final: 0.8133 (mttt) REVERT: B 90 LYS cc_start: 0.8470 (mttt) cc_final: 0.8175 (mttt) REVERT: B 94 ILE cc_start: 0.8274 (mt) cc_final: 0.8021 (mm) REVERT: B 98 VAL cc_start: 0.8623 (t) cc_final: 0.8150 (t) REVERT: B 101 TYR cc_start: 0.8579 (t80) cc_final: 0.8331 (t80) REVERT: B 104 ARG cc_start: 0.8731 (tpt90) cc_final: 0.8449 (tpt90) REVERT: B 107 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7368 (mt-10) REVERT: B 112 LEU cc_start: 0.8271 (mp) cc_final: 0.7512 (mp) REVERT: B 125 LYS cc_start: 0.8866 (mttt) cc_final: 0.8336 (mtpp) REVERT: B 132 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8033 (mtm180) REVERT: B 137 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7449 (mtp-110) REVERT: B 141 SER cc_start: 0.8543 (m) cc_final: 0.8061 (p) REVERT: B 151 MET cc_start: 0.7891 (mtp) cc_final: 0.7488 (mtp) REVERT: B 152 MET cc_start: 0.8026 (tpt) cc_final: 0.7788 (tpt) REVERT: B 155 ILE cc_start: 0.9254 (mm) cc_final: 0.9040 (mm) REVERT: B 169 ASN cc_start: 0.8843 (m-40) cc_final: 0.8369 (t0) REVERT: B 175 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 183 GLU cc_start: 0.8539 (mp0) cc_final: 0.8263 (mp0) REVERT: B 190 GLU cc_start: 0.8163 (tt0) cc_final: 0.7902 (tt0) REVERT: B 193 GLU cc_start: 0.8371 (tt0) cc_final: 0.8121 (tt0) REVERT: B 196 LEU cc_start: 0.8750 (mt) cc_final: 0.8430 (tp) REVERT: B 202 LEU cc_start: 0.7692 (mm) cc_final: 0.7218 (tp) REVERT: B 207 VAL cc_start: 0.8847 (t) cc_final: 0.8583 (p) REVERT: B 212 GLU cc_start: 0.7885 (tp30) cc_final: 0.7653 (tp30) REVERT: B 213 GLU cc_start: 0.8165 (tt0) cc_final: 0.7699 (tt0) REVERT: B 215 CYS cc_start: 0.8304 (t) cc_final: 0.7793 (t) REVERT: B 228 LYS cc_start: 0.8550 (ttpt) cc_final: 0.7989 (ttpt) REVERT: B 244 ILE cc_start: 0.9068 (mt) cc_final: 0.8637 (tp) REVERT: B 246 HIS cc_start: 0.8403 (m-70) cc_final: 0.8162 (m-70) REVERT: B 247 MET cc_start: 0.7240 (tmm) cc_final: 0.6715 (tmm) REVERT: B 298 ARG cc_start: 0.8581 (mmm160) cc_final: 0.7723 (mpt180) REVERT: B 305 LYS cc_start: 0.8715 (tttt) cc_final: 0.8382 (ttpp) REVERT: B 308 LEU cc_start: 0.8558 (mt) cc_final: 0.8250 (mm) REVERT: B 311 ARG cc_start: 0.8344 (ptt180) cc_final: 0.7652 (ptt-90) REVERT: B 317 MET cc_start: 0.8697 (tpp) cc_final: 0.8383 (tpp) REVERT: B 321 GLN cc_start: 0.8062 (tt0) cc_final: 0.7608 (tt0) REVERT: B 326 ILE cc_start: 0.8021 (mm) cc_final: 0.7720 (mm) REVERT: B 341 ARG cc_start: 0.8752 (ptt90) cc_final: 0.7933 (ttp80) REVERT: B 346 ASN cc_start: 0.7104 (p0) cc_final: 0.6505 (p0) REVERT: B 387 THR cc_start: 0.8368 (m) cc_final: 0.8084 (m) REVERT: B 388 LEU cc_start: 0.8705 (mt) cc_final: 0.8405 (mm) REVERT: B 391 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7164 (mt-10) REVERT: M 1 MET cc_start: 0.7116 (mpp) cc_final: 0.6511 (mpp) REVERT: M 17 GLU cc_start: 0.7555 (pt0) cc_final: 0.7330 (pt0) REVERT: M 21 LYS cc_start: 0.7929 (mttt) cc_final: 0.7263 (mttp) REVERT: M 29 CYS cc_start: 0.8608 (t) cc_final: 0.8231 (t) REVERT: M 34 GLU cc_start: 0.8986 (tt0) cc_final: 0.8714 (tt0) REVERT: M 43 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7360 (mt-10) REVERT: M 64 LEU cc_start: 0.8579 (tp) cc_final: 0.8333 (tp) REVERT: M 88 ASP cc_start: 0.8546 (m-30) cc_final: 0.8332 (m-30) REVERT: M 89 THR cc_start: 0.8937 (m) cc_final: 0.8574 (p) REVERT: M 92 ASP cc_start: 0.8009 (t0) cc_final: 0.7735 (t0) REVERT: M 108 ILE cc_start: 0.8868 (mt) cc_final: 0.8667 (mt) REVERT: M 116 MET cc_start: 0.7951 (mtm) cc_final: 0.7529 (mtm) REVERT: M 119 ASN cc_start: 0.8166 (t0) cc_final: 0.7670 (t0) REVERT: M 123 LEU cc_start: 0.8641 (tp) cc_final: 0.8430 (tp) REVERT: M 126 GLU cc_start: 0.8160 (tp30) cc_final: 0.7606 (tp30) REVERT: M 128 ASN cc_start: 0.8301 (m-40) cc_final: 0.8001 (m110) REVERT: M 131 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8004 (mttp) REVERT: M 134 ILE cc_start: 0.8358 (mt) cc_final: 0.8109 (mt) REVERT: M 135 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8406 (mmtt) REVERT: M 157 LEU cc_start: 0.8448 (mt) cc_final: 0.8189 (pp) REVERT: M 159 THR cc_start: 0.8187 (m) cc_final: 0.7825 (t) REVERT: M 161 GLN cc_start: 0.8286 (tp40) cc_final: 0.8052 (tp-100) REVERT: M 183 VAL cc_start: 0.8571 (t) cc_final: 0.8294 (p) REVERT: M 203 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6973 (mm-40) REVERT: M 209 CYS cc_start: 0.7348 (t) cc_final: 0.6347 (m) REVERT: M 220 LEU cc_start: 0.8209 (mm) cc_final: 0.7777 (mm) REVERT: M 227 LEU cc_start: 0.8942 (mt) cc_final: 0.8546 (mp) REVERT: M 240 LYS cc_start: 0.8457 (mttt) cc_final: 0.7961 (mttt) REVERT: M 242 TRP cc_start: 0.7492 (t-100) cc_final: 0.7147 (t-100) REVERT: M 245 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6358 (mm-30) REVERT: M 251 ILE cc_start: 0.8545 (mm) cc_final: 0.8345 (mm) REVERT: M 257 PHE cc_start: 0.8416 (p90) cc_final: 0.8086 (p90) REVERT: M 258 ARG cc_start: 0.8324 (mtm180) cc_final: 0.8062 (mtm-85) REVERT: M 262 TYR cc_start: 0.8407 (p90) cc_final: 0.7968 (p90) REVERT: M 298 LYS cc_start: 0.9002 (tttt) cc_final: 0.8631 (tttt) REVERT: M 300 ASN cc_start: 0.9081 (p0) cc_final: 0.8860 (p0) REVERT: M 377 PHE cc_start: 0.7931 (p90) cc_final: 0.7433 (p90) REVERT: M 393 ASP cc_start: 0.8037 (t0) cc_final: 0.7578 (t0) REVERT: M 402 PHE cc_start: 0.7744 (m-80) cc_final: 0.7224 (m-10) REVERT: M 414 PHE cc_start: 0.7807 (t80) cc_final: 0.7226 (t80) REVERT: C 23 VAL cc_start: 0.8745 (m) cc_final: 0.8344 (m) REVERT: C 58 TYR cc_start: 0.8074 (t80) cc_final: 0.7682 (t80) REVERT: C 64 THR cc_start: 0.6668 (m) cc_final: 0.6446 (t) REVERT: C 68 VAL cc_start: 0.8260 (t) cc_final: 0.8001 (p) REVERT: C 78 TRP cc_start: 0.8244 (m-10) cc_final: 0.7925 (m-10) REVERT: C 84 ASN cc_start: 0.8537 (t0) cc_final: 0.7914 (t0) REVERT: C 95 ASN cc_start: 0.7717 (t0) cc_final: 0.7461 (t0) REVERT: C 142 LYS cc_start: 0.8926 (mttm) cc_final: 0.8637 (mttm) REVERT: C 145 LEU cc_start: 0.8224 (mt) cc_final: 0.7907 (mt) REVERT: C 151 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8374 (tpt170) REVERT: C 153 TRP cc_start: 0.8608 (p-90) cc_final: 0.8104 (p-90) REVERT: C 167 TYR cc_start: 0.7922 (m-10) cc_final: 0.7108 (m-10) REVERT: C 168 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7695 (mt-10) REVERT: C 171 ASP cc_start: 0.8219 (m-30) cc_final: 0.7841 (m-30) REVERT: b 43 LYS cc_start: 0.8244 (mttt) cc_final: 0.7708 (tttp) REVERT: b 45 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7156 (mm-30) REVERT: b 47 LEU cc_start: 0.8994 (mt) cc_final: 0.8680 (mt) REVERT: b 48 LYS cc_start: 0.8821 (ptpp) cc_final: 0.7964 (pttm) REVERT: b 66 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8103 (mp) REVERT: b 72 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8266 (mtmt) REVERT: b 74 LYS cc_start: 0.8533 (tppt) cc_final: 0.8325 (mmtp) REVERT: b 80 PHE cc_start: 0.8547 (t80) cc_final: 0.7876 (t80) REVERT: b 85 LYS cc_start: 0.8601 (mttt) cc_final: 0.8160 (mttt) REVERT: b 101 TYR cc_start: 0.8737 (t80) cc_final: 0.8488 (t80) REVERT: b 132 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8126 (mtm180) REVERT: b 141 SER cc_start: 0.8536 (m) cc_final: 0.8242 (m) REVERT: b 142 ILE cc_start: 0.9037 (mm) cc_final: 0.8740 (mp) REVERT: b 150 ILE cc_start: 0.8194 (mt) cc_final: 0.7970 (mt) REVERT: b 151 MET cc_start: 0.7640 (mtp) cc_final: 0.7196 (mtp) REVERT: b 152 MET cc_start: 0.8070 (tpt) cc_final: 0.7829 (tpt) REVERT: b 175 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8163 (tm-30) REVERT: b 181 ASP cc_start: 0.8281 (t0) cc_final: 0.7846 (t0) REVERT: b 186 GLU cc_start: 0.8303 (pm20) cc_final: 0.8049 (pm20) REVERT: b 187 MET cc_start: 0.8201 (mtm) cc_final: 0.7934 (mtm) REVERT: b 190 GLU cc_start: 0.8067 (tt0) cc_final: 0.7860 (tt0) REVERT: b 195 LEU cc_start: 0.9074 (mt) cc_final: 0.8722 (mt) REVERT: b 199 LYS cc_start: 0.8264 (mppt) cc_final: 0.8016 (mmtm) REVERT: b 202 LEU cc_start: 0.7709 (mm) cc_final: 0.7310 (tp) REVERT: b 207 VAL cc_start: 0.8891 (t) cc_final: 0.8456 (p) REVERT: b 212 GLU cc_start: 0.8113 (tp30) cc_final: 0.7894 (tp30) REVERT: b 213 GLU cc_start: 0.8294 (tt0) cc_final: 0.7626 (tt0) REVERT: b 215 CYS cc_start: 0.8399 (t) cc_final: 0.7876 (t) REVERT: b 228 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8065 (ttpt) REVERT: b 244 ILE cc_start: 0.9092 (mt) cc_final: 0.8656 (tp) REVERT: b 247 MET cc_start: 0.7461 (tmm) cc_final: 0.5990 (tmm) REVERT: b 298 ARG cc_start: 0.8815 (mmm160) cc_final: 0.7429 (mpt180) REVERT: b 307 LEU cc_start: 0.8917 (mt) cc_final: 0.8529 (mt) REVERT: b 308 LEU cc_start: 0.8693 (mt) cc_final: 0.8340 (mm) REVERT: b 311 ARG cc_start: 0.8344 (ptt180) cc_final: 0.7722 (ptt-90) REVERT: b 317 MET cc_start: 0.8682 (tpp) cc_final: 0.8419 (tpt) REVERT: b 321 GLN cc_start: 0.7909 (tt0) cc_final: 0.7515 (tt0) REVERT: b 322 LEU cc_start: 0.8442 (tt) cc_final: 0.8224 (tt) REVERT: b 324 TRP cc_start: 0.8751 (t-100) cc_final: 0.8030 (t-100) REVERT: b 326 ILE cc_start: 0.8011 (mm) cc_final: 0.7754 (mm) REVERT: b 341 ARG cc_start: 0.8716 (ptt90) cc_final: 0.7968 (ttp80) REVERT: b 346 ASN cc_start: 0.7083 (p0) cc_final: 0.6809 (p0) REVERT: b 351 TYR cc_start: 0.8000 (t80) cc_final: 0.7706 (t80) REVERT: b 352 ILE cc_start: 0.8675 (mm) cc_final: 0.8436 (mm) REVERT: b 355 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: b 384 MET cc_start: 0.7998 (ptt) cc_final: 0.7430 (ptt) REVERT: b 386 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8267 (mtpt) REVERT: b 417 ASP cc_start: 0.7859 (t0) cc_final: 0.7410 (t0) REVERT: m 1 MET cc_start: 0.7015 (mtt) cc_final: 0.6505 (mtt) REVERT: m 17 GLU cc_start: 0.7526 (pt0) cc_final: 0.7246 (pt0) REVERT: m 29 CYS cc_start: 0.8474 (m) cc_final: 0.7914 (t) REVERT: m 36 GLN cc_start: 0.8373 (tp40) cc_final: 0.7984 (tp40) REVERT: m 37 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8440 (tm-30) REVERT: m 43 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7452 (mt-10) REVERT: m 44 ASN cc_start: 0.8160 (t0) cc_final: 0.7442 (t0) REVERT: m 45 VAL cc_start: 0.8853 (t) cc_final: 0.8612 (t) REVERT: m 71 GLN cc_start: 0.8383 (tp40) cc_final: 0.7877 (tp40) REVERT: m 74 VAL cc_start: 0.9040 (t) cc_final: 0.8726 (p) REVERT: m 77 LEU cc_start: 0.8536 (mt) cc_final: 0.8303 (mt) REVERT: m 78 PHE cc_start: 0.8741 (t80) cc_final: 0.8312 (t80) REVERT: m 80 ILE cc_start: 0.8532 (mt) cc_final: 0.8215 (mm) REVERT: m 81 GLU cc_start: 0.7741 (tp30) cc_final: 0.7376 (tp30) REVERT: m 88 ASP cc_start: 0.8654 (m-30) cc_final: 0.8345 (m-30) REVERT: m 89 THR cc_start: 0.8973 (m) cc_final: 0.8542 (p) REVERT: m 90 PHE cc_start: 0.8761 (m-10) cc_final: 0.8558 (m-10) REVERT: m 103 LYS cc_start: 0.7301 (mtmm) cc_final: 0.7014 (mtmm) REVERT: m 111 GLU cc_start: 0.7951 (tt0) cc_final: 0.7603 (tt0) REVERT: m 115 GLU cc_start: 0.8452 (tp30) cc_final: 0.7805 (tp30) REVERT: m 116 MET cc_start: 0.7671 (mtm) cc_final: 0.7468 (mtm) REVERT: m 126 GLU cc_start: 0.8219 (tp30) cc_final: 0.7428 (tp30) REVERT: m 128 ASN cc_start: 0.8333 (m-40) cc_final: 0.7667 (m-40) REVERT: m 129 ILE cc_start: 0.8907 (mm) cc_final: 0.8590 (tp) REVERT: m 134 ILE cc_start: 0.8254 (mt) cc_final: 0.7646 (tp) REVERT: m 140 LEU cc_start: 0.8519 (mt) cc_final: 0.8247 (tt) REVERT: m 141 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7766 (mmt90) REVERT: m 161 GLN cc_start: 0.8366 (tp40) cc_final: 0.8148 (tp-100) REVERT: m 172 VAL cc_start: 0.8792 (t) cc_final: 0.8444 (m) REVERT: m 209 CYS cc_start: 0.7318 (t) cc_final: 0.6348 (m) REVERT: m 234 HIS cc_start: 0.7915 (t-90) cc_final: 0.7711 (t-90) REVERT: m 240 LYS cc_start: 0.8624 (mttt) cc_final: 0.8029 (mmmm) REVERT: m 243 GLU cc_start: 0.8581 (tp30) cc_final: 0.8137 (tp30) REVERT: m 257 PHE cc_start: 0.8523 (p90) cc_final: 0.8226 (p90) REVERT: m 258 ARG cc_start: 0.8322 (mtm180) cc_final: 0.8082 (mtm-85) REVERT: m 262 TYR cc_start: 0.8221 (p90) cc_final: 0.7152 (p90) REVERT: m 298 LYS cc_start: 0.9071 (tttt) cc_final: 0.8676 (tttt) REVERT: m 300 ASN cc_start: 0.9082 (p0) cc_final: 0.8847 (p0) REVERT: m 377 PHE cc_start: 0.7822 (p90) cc_final: 0.7493 (p90) REVERT: m 393 ASP cc_start: 0.8206 (t0) cc_final: 0.7970 (t0) REVERT: m 402 PHE cc_start: 0.7521 (m-80) cc_final: 0.7083 (m-80) REVERT: m 406 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8408 (ttmt) REVERT: m 407 TYR cc_start: 0.8636 (m-80) cc_final: 0.8031 (m-80) REVERT: m 414 PHE cc_start: 0.7886 (t80) cc_final: 0.7439 (t80) REVERT: c 18 MET cc_start: 0.6352 (mmt) cc_final: 0.6068 (mmt) REVERT: c 58 TYR cc_start: 0.8141 (t80) cc_final: 0.7573 (t80) REVERT: c 64 THR cc_start: 0.6564 (m) cc_final: 0.6314 (t) REVERT: c 78 TRP cc_start: 0.8270 (m-10) cc_final: 0.7552 (m-10) REVERT: c 81 TYR cc_start: 0.7197 (m-80) cc_final: 0.6545 (m-80) REVERT: c 82 PHE cc_start: 0.8205 (m-80) cc_final: 0.7845 (m-80) REVERT: c 84 ASN cc_start: 0.8240 (t0) cc_final: 0.7599 (t0) REVERT: c 110 MET cc_start: 0.8538 (mmm) cc_final: 0.7836 (mmm) REVERT: c 115 GLU cc_start: 0.7761 (tt0) cc_final: 0.7493 (tt0) REVERT: c 134 MET cc_start: 0.5826 (mmt) cc_final: 0.5547 (mpp) REVERT: c 135 ASN cc_start: 0.8018 (p0) cc_final: 0.7481 (p0) REVERT: c 145 LEU cc_start: 0.8290 (mt) cc_final: 0.7923 (mt) REVERT: c 152 ASN cc_start: 0.7823 (t0) cc_final: 0.7283 (t0) REVERT: c 153 TRP cc_start: 0.8687 (p-90) cc_final: 0.8186 (p-90) REVERT: c 159 CYS cc_start: 0.8448 (t) cc_final: 0.8203 (t) REVERT: c 167 TYR cc_start: 0.8042 (m-10) cc_final: 0.7231 (m-10) REVERT: c 168 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7670 (mt-10) REVERT: c 171 ASP cc_start: 0.8232 (m-30) cc_final: 0.7899 (m-30) REVERT: c 178 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7677 (ttm170) outliers start: 2 outliers final: 0 residues processed: 782 average time/residue: 0.3257 time to fit residues: 358.2365 Evaluate side-chains 747 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 745 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 148 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN M 71 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 GLN m 36 GLN m 54 HIS ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115406 restraints weight = 31254.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119639 restraints weight = 16992.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122463 restraints weight = 10641.585| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16108 Z= 0.200 Angle : 0.582 8.248 21822 Z= 0.306 Chirality : 0.045 0.166 2524 Planarity : 0.004 0.054 2752 Dihedral : 10.351 170.037 2154 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.13 % 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: 1.23 (0.20), residues: 1954 helix: 1.18 (0.18), residues: 810 sheet: 0.20 (0.27), residues: 368 loop : 0.99 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 172 HIS 0.009 0.001 HIS M 3 PHE 0.026 0.002 PHE C 82 TYR 0.022 0.002 TYR b 351 ARG 0.007 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 764 time to evaluate : 2.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8259 (mttt) cc_final: 0.7579 (mmmt) REVERT: B 47 LEU cc_start: 0.9038 (mt) cc_final: 0.8607 (mt) REVERT: B 50 MET cc_start: 0.8655 (mtm) cc_final: 0.8126 (mtm) REVERT: B 51 LEU cc_start: 0.8757 (mt) cc_final: 0.8447 (mt) REVERT: B 52 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7547 (mm-30) REVERT: B 54 ASN cc_start: 0.7859 (m110) cc_final: 0.7464 (m110) REVERT: B 59 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8255 (ptpp) REVERT: B 63 MET cc_start: 0.8499 (mmm) cc_final: 0.7990 (mmm) REVERT: B 66 ILE cc_start: 0.8658 (mm) cc_final: 0.8360 (mm) REVERT: B 72 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8484 (mtpt) REVERT: B 74 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8265 (mmtt) REVERT: B 80 PHE cc_start: 0.8563 (t80) cc_final: 0.7715 (t80) REVERT: B 83 VAL cc_start: 0.8296 (t) cc_final: 0.8093 (t) REVERT: B 84 VAL cc_start: 0.8561 (p) cc_final: 0.8272 (m) REVERT: B 85 LYS cc_start: 0.8580 (mttt) cc_final: 0.7882 (mttt) REVERT: B 90 LYS cc_start: 0.8514 (mttt) cc_final: 0.8223 (mttt) REVERT: B 98 VAL cc_start: 0.8653 (t) cc_final: 0.8412 (t) REVERT: B 101 TYR cc_start: 0.8534 (t80) cc_final: 0.8299 (t80) REVERT: B 107 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 112 LEU cc_start: 0.8282 (mp) cc_final: 0.7499 (mp) REVERT: B 121 GLN cc_start: 0.8362 (tt0) cc_final: 0.8119 (tt0) REVERT: B 125 LYS cc_start: 0.8897 (mttt) cc_final: 0.8392 (mtpp) REVERT: B 132 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7997 (mtm180) REVERT: B 137 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7298 (mtp-110) REVERT: B 147 ILE cc_start: 0.8465 (pt) cc_final: 0.7756 (pt) REVERT: B 151 MET cc_start: 0.7815 (mtp) cc_final: 0.7049 (mtp) REVERT: B 155 ILE cc_start: 0.9239 (mm) cc_final: 0.8978 (mm) REVERT: B 169 ASN cc_start: 0.8680 (m-40) cc_final: 0.8220 (t0) REVERT: B 175 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 190 GLU cc_start: 0.8132 (tt0) cc_final: 0.7875 (tt0) REVERT: B 193 GLU cc_start: 0.8376 (tt0) cc_final: 0.8120 (tt0) REVERT: B 196 LEU cc_start: 0.8789 (mt) cc_final: 0.8498 (tp) REVERT: B 199 LYS cc_start: 0.8021 (mppt) cc_final: 0.7774 (mmtm) REVERT: B 202 LEU cc_start: 0.7642 (mm) cc_final: 0.7168 (tp) REVERT: B 207 VAL cc_start: 0.8796 (t) cc_final: 0.8542 (p) REVERT: B 213 GLU cc_start: 0.8053 (tt0) cc_final: 0.7636 (tt0) REVERT: B 228 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8040 (ttpt) REVERT: B 244 ILE cc_start: 0.9039 (mt) cc_final: 0.8620 (tp) REVERT: B 246 HIS cc_start: 0.8478 (m-70) cc_final: 0.8206 (m-70) REVERT: B 247 MET cc_start: 0.7206 (tmm) cc_final: 0.6693 (tmm) REVERT: B 298 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8173 (mpt180) REVERT: B 302 ARG cc_start: 0.8534 (ttm110) cc_final: 0.7744 (mpt180) REVERT: B 305 LYS cc_start: 0.8775 (tttt) cc_final: 0.8454 (ttpp) REVERT: B 308 LEU cc_start: 0.8635 (mt) cc_final: 0.8283 (mm) REVERT: B 311 ARG cc_start: 0.8268 (ptt180) cc_final: 0.7565 (ptt-90) REVERT: B 317 MET cc_start: 0.8594 (tpp) cc_final: 0.8221 (tpp) REVERT: B 321 GLN cc_start: 0.8030 (tt0) cc_final: 0.7548 (tt0) REVERT: B 322 LEU cc_start: 0.8421 (tt) cc_final: 0.8206 (tt) REVERT: B 326 ILE cc_start: 0.7970 (mm) cc_final: 0.7673 (mm) REVERT: B 341 ARG cc_start: 0.8702 (ptt90) cc_final: 0.8050 (ptm-80) REVERT: B 346 ASN cc_start: 0.7153 (p0) cc_final: 0.6651 (p0) REVERT: B 351 TYR cc_start: 0.7938 (t80) cc_final: 0.7441 (t80) REVERT: B 387 THR cc_start: 0.8365 (m) cc_final: 0.8051 (m) REVERT: B 388 LEU cc_start: 0.8775 (mt) cc_final: 0.8453 (mm) REVERT: B 391 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7152 (mt-10) REVERT: M 1 MET cc_start: 0.7137 (mpp) cc_final: 0.6197 (mpp) REVERT: M 17 GLU cc_start: 0.7556 (pt0) cc_final: 0.7225 (pt0) REVERT: M 29 CYS cc_start: 0.8664 (t) cc_final: 0.8258 (t) REVERT: M 34 GLU cc_start: 0.8963 (tt0) cc_final: 0.8715 (tt0) REVERT: M 43 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7444 (mt-10) REVERT: M 77 LEU cc_start: 0.8534 (mt) cc_final: 0.8108 (mt) REVERT: M 88 ASP cc_start: 0.8600 (m-30) cc_final: 0.8320 (m-30) REVERT: M 89 THR cc_start: 0.9038 (m) cc_final: 0.8724 (p) REVERT: M 92 ASP cc_start: 0.8034 (t0) cc_final: 0.7833 (t0) REVERT: M 116 MET cc_start: 0.7843 (mtm) cc_final: 0.7525 (mtm) REVERT: M 126 GLU cc_start: 0.8186 (tp30) cc_final: 0.7659 (tp30) REVERT: M 131 LYS cc_start: 0.8502 (mtmm) cc_final: 0.7938 (mttp) REVERT: M 134 ILE cc_start: 0.8436 (mt) cc_final: 0.8193 (mt) REVERT: M 135 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8415 (mmtt) REVERT: M 157 LEU cc_start: 0.8512 (mt) cc_final: 0.8263 (pp) REVERT: M 159 THR cc_start: 0.8200 (m) cc_final: 0.7943 (p) REVERT: M 161 GLN cc_start: 0.8396 (tp40) cc_final: 0.8144 (tp-100) REVERT: M 183 VAL cc_start: 0.8627 (t) cc_final: 0.8344 (p) REVERT: M 203 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6901 (mm-40) REVERT: M 209 CYS cc_start: 0.7356 (t) cc_final: 0.6518 (m) REVERT: M 220 LEU cc_start: 0.8275 (mm) cc_final: 0.7845 (mm) REVERT: M 227 LEU cc_start: 0.8956 (mt) cc_final: 0.8576 (mp) REVERT: M 242 TRP cc_start: 0.7629 (t-100) cc_final: 0.7281 (t-100) REVERT: M 245 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6283 (mm-30) REVERT: M 257 PHE cc_start: 0.8430 (p90) cc_final: 0.8097 (p90) REVERT: M 258 ARG cc_start: 0.8361 (mtm180) cc_final: 0.8056 (mtm-85) REVERT: M 262 TYR cc_start: 0.8387 (p90) cc_final: 0.8011 (p90) REVERT: M 298 LYS cc_start: 0.9028 (tttt) cc_final: 0.8657 (tttt) REVERT: M 300 ASN cc_start: 0.9074 (p0) cc_final: 0.8840 (p0) REVERT: M 377 PHE cc_start: 0.7823 (p90) cc_final: 0.7451 (p90) REVERT: M 393 ASP cc_start: 0.7946 (t0) cc_final: 0.7526 (t0) REVERT: M 402 PHE cc_start: 0.7755 (m-80) cc_final: 0.7188 (m-80) REVERT: M 414 PHE cc_start: 0.7798 (t80) cc_final: 0.7274 (t80) REVERT: C 23 VAL cc_start: 0.8755 (m) cc_final: 0.8334 (m) REVERT: C 44 THR cc_start: 0.9173 (m) cc_final: 0.8796 (p) REVERT: C 68 VAL cc_start: 0.8220 (t) cc_final: 0.7928 (p) REVERT: C 78 TRP cc_start: 0.8288 (m-10) cc_final: 0.8068 (m-10) REVERT: C 81 TYR cc_start: 0.7141 (m-80) cc_final: 0.6451 (m-80) REVERT: C 82 PHE cc_start: 0.8177 (m-80) cc_final: 0.7294 (m-80) REVERT: C 84 ASN cc_start: 0.8551 (t0) cc_final: 0.7868 (t0) REVERT: C 95 ASN cc_start: 0.7708 (t0) cc_final: 0.7469 (t0) REVERT: C 110 MET cc_start: 0.8539 (mmm) cc_final: 0.8126 (mmm) REVERT: C 115 GLU cc_start: 0.7851 (tt0) cc_final: 0.7614 (tt0) REVERT: C 142 LYS cc_start: 0.8919 (mttm) cc_final: 0.8660 (mttm) REVERT: C 145 LEU cc_start: 0.8072 (mt) cc_final: 0.7797 (mt) REVERT: C 168 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7526 (mt-10) REVERT: C 171 ASP cc_start: 0.8087 (m-30) cc_final: 0.7784 (m-30) REVERT: C 172 TRP cc_start: 0.8304 (t60) cc_final: 0.7488 (t60) REVERT: b 43 LYS cc_start: 0.8159 (mttt) cc_final: 0.7736 (tttp) REVERT: b 45 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7177 (mm-30) REVERT: b 48 LYS cc_start: 0.8958 (ptpp) cc_final: 0.8393 (pttm) REVERT: b 54 ASN cc_start: 0.7975 (m110) cc_final: 0.7536 (m110) REVERT: b 55 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8068 (mtpt) REVERT: b 63 MET cc_start: 0.8561 (mmm) cc_final: 0.7931 (mmm) REVERT: b 66 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8068 (mp) REVERT: b 72 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8258 (mtmt) REVERT: b 80 PHE cc_start: 0.8488 (t80) cc_final: 0.7910 (t80) REVERT: b 83 VAL cc_start: 0.8184 (t) cc_final: 0.7913 (t) REVERT: b 85 LYS cc_start: 0.8594 (mttt) cc_final: 0.8099 (mttt) REVERT: b 98 VAL cc_start: 0.8713 (t) cc_final: 0.8457 (t) REVERT: b 107 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7435 (mt-10) REVERT: b 121 GLN cc_start: 0.8162 (tt0) cc_final: 0.7954 (mt0) REVERT: b 128 ASN cc_start: 0.8346 (t0) cc_final: 0.8077 (t0) REVERT: b 132 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8130 (mtm180) REVERT: b 147 ILE cc_start: 0.8416 (pt) cc_final: 0.7688 (pt) REVERT: b 150 ILE cc_start: 0.8233 (mt) cc_final: 0.7977 (mt) REVERT: b 151 MET cc_start: 0.7546 (mtp) cc_final: 0.6843 (mtp) REVERT: b 162 LEU cc_start: 0.7853 (mp) cc_final: 0.7044 (tp) REVERT: b 175 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8033 (tm-30) REVERT: b 187 MET cc_start: 0.8224 (mtm) cc_final: 0.7944 (mtm) REVERT: b 190 GLU cc_start: 0.8076 (tt0) cc_final: 0.7864 (tt0) REVERT: b 195 LEU cc_start: 0.9061 (mt) cc_final: 0.8738 (mt) REVERT: b 202 LEU cc_start: 0.7690 (mm) cc_final: 0.7295 (tp) REVERT: b 207 VAL cc_start: 0.8802 (t) cc_final: 0.8511 (p) REVERT: b 212 GLU cc_start: 0.8173 (tp30) cc_final: 0.7730 (tp30) REVERT: b 213 GLU cc_start: 0.8260 (tt0) cc_final: 0.7663 (tt0) REVERT: b 218 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8734 (mtp85) REVERT: b 228 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8148 (ttpt) REVERT: b 244 ILE cc_start: 0.9106 (mt) cc_final: 0.8684 (tp) REVERT: b 247 MET cc_start: 0.7288 (tmm) cc_final: 0.6794 (tmm) REVERT: b 298 ARG cc_start: 0.8876 (mmm160) cc_final: 0.7986 (mpt180) REVERT: b 302 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8143 (mpt180) REVERT: b 307 LEU cc_start: 0.8892 (mt) cc_final: 0.8422 (mt) REVERT: b 308 LEU cc_start: 0.8725 (mt) cc_final: 0.8415 (mm) REVERT: b 311 ARG cc_start: 0.8316 (ptt180) cc_final: 0.7808 (ptt-90) REVERT: b 317 MET cc_start: 0.8643 (tpp) cc_final: 0.8268 (tpp) REVERT: b 321 GLN cc_start: 0.7994 (tt0) cc_final: 0.7405 (tt0) REVERT: b 324 TRP cc_start: 0.8698 (t-100) cc_final: 0.8062 (t-100) REVERT: b 326 ILE cc_start: 0.8008 (mm) cc_final: 0.7792 (mm) REVERT: b 331 GLU cc_start: 0.7135 (mp0) cc_final: 0.6808 (mp0) REVERT: b 341 ARG cc_start: 0.8627 (ptt90) cc_final: 0.7912 (ttp80) REVERT: b 346 ASN cc_start: 0.7165 (p0) cc_final: 0.6808 (p0) REVERT: b 384 MET cc_start: 0.7929 (ptt) cc_final: 0.7393 (ptt) REVERT: b 629 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7955 (ttmt) REVERT: m 1 MET cc_start: 0.6956 (mtt) cc_final: 0.6670 (mtt) REVERT: m 17 GLU cc_start: 0.7518 (pt0) cc_final: 0.7248 (pt0) REVERT: m 21 LYS cc_start: 0.7957 (mttt) cc_final: 0.7437 (mttm) REVERT: m 29 CYS cc_start: 0.8449 (m) cc_final: 0.7866 (t) REVERT: m 36 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7979 (tp-100) REVERT: m 37 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8475 (tm-30) REVERT: m 43 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7466 (mt-10) REVERT: m 44 ASN cc_start: 0.8258 (t0) cc_final: 0.7520 (t0) REVERT: m 45 VAL cc_start: 0.8876 (t) cc_final: 0.8635 (t) REVERT: m 71 GLN cc_start: 0.8367 (tp40) cc_final: 0.7886 (tp-100) REVERT: m 72 THR cc_start: 0.8598 (p) cc_final: 0.8150 (t) REVERT: m 77 LEU cc_start: 0.8565 (mt) cc_final: 0.8311 (mt) REVERT: m 78 PHE cc_start: 0.8786 (t80) cc_final: 0.8333 (t80) REVERT: m 80 ILE cc_start: 0.8540 (mt) cc_final: 0.8244 (mm) REVERT: m 88 ASP cc_start: 0.8588 (m-30) cc_final: 0.8308 (m-30) REVERT: m 89 THR cc_start: 0.8877 (m) cc_final: 0.8606 (p) REVERT: m 90 PHE cc_start: 0.8749 (m-10) cc_final: 0.8547 (m-10) REVERT: m 111 GLU cc_start: 0.7978 (tt0) cc_final: 0.7631 (tt0) REVERT: m 116 MET cc_start: 0.7660 (mtm) cc_final: 0.7297 (mtm) REVERT: m 125 THR cc_start: 0.8776 (m) cc_final: 0.8386 (t) REVERT: m 128 ASN cc_start: 0.8267 (m-40) cc_final: 0.8048 (m-40) REVERT: m 129 ILE cc_start: 0.8926 (mm) cc_final: 0.8622 (tp) REVERT: m 131 LYS cc_start: 0.8714 (mttp) cc_final: 0.8414 (mttt) REVERT: m 134 ILE cc_start: 0.8108 (mt) cc_final: 0.7403 (tp) REVERT: m 140 LEU cc_start: 0.8495 (mt) cc_final: 0.8206 (tt) REVERT: m 141 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7705 (mmt90) REVERT: m 161 GLN cc_start: 0.8346 (tp40) cc_final: 0.8124 (tp-100) REVERT: m 209 CYS cc_start: 0.7332 (t) cc_final: 0.6480 (m) REVERT: m 220 LEU cc_start: 0.8201 (mm) cc_final: 0.7851 (mm) REVERT: m 240 LYS cc_start: 0.8580 (mttt) cc_final: 0.7998 (mmmm) REVERT: m 243 GLU cc_start: 0.8545 (tp30) cc_final: 0.8119 (tp30) REVERT: m 257 PHE cc_start: 0.8514 (p90) cc_final: 0.8200 (p90) REVERT: m 258 ARG cc_start: 0.8377 (mtm180) cc_final: 0.8017 (mtm180) REVERT: m 262 TYR cc_start: 0.8185 (p90) cc_final: 0.7119 (p90) REVERT: m 298 LYS cc_start: 0.9074 (tttt) cc_final: 0.8724 (tttt) REVERT: m 300 ASN cc_start: 0.9073 (p0) cc_final: 0.8750 (p0) REVERT: m 342 ASP cc_start: 0.7960 (t0) cc_final: 0.7581 (t0) REVERT: m 377 PHE cc_start: 0.7691 (p90) cc_final: 0.7471 (p90) REVERT: m 393 ASP cc_start: 0.8102 (t0) cc_final: 0.7830 (t0) REVERT: m 402 PHE cc_start: 0.7605 (m-80) cc_final: 0.7116 (m-80) REVERT: m 406 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8363 (ttmt) REVERT: m 407 TYR cc_start: 0.8682 (m-80) cc_final: 0.8027 (m-80) REVERT: m 414 PHE cc_start: 0.7890 (t80) cc_final: 0.7448 (t80) REVERT: c 58 TYR cc_start: 0.8089 (t80) cc_final: 0.7585 (t80) REVERT: c 64 THR cc_start: 0.6646 (m) cc_final: 0.6355 (t) REVERT: c 78 TRP cc_start: 0.8293 (m-10) cc_final: 0.7565 (m-10) REVERT: c 81 TYR cc_start: 0.7176 (m-80) cc_final: 0.6510 (m-80) REVERT: c 82 PHE cc_start: 0.8181 (m-10) cc_final: 0.7908 (m-80) REVERT: c 84 ASN cc_start: 0.8265 (t0) cc_final: 0.7498 (t0) REVERT: c 110 MET cc_start: 0.8494 (mmm) cc_final: 0.7843 (mmm) REVERT: c 115 GLU cc_start: 0.7789 (tt0) cc_final: 0.7555 (tt0) REVERT: c 145 LEU cc_start: 0.8302 (mt) cc_final: 0.7961 (mt) REVERT: c 152 ASN cc_start: 0.7826 (t0) cc_final: 0.7602 (t0) REVERT: c 167 TYR cc_start: 0.8057 (m-10) cc_final: 0.7240 (m-10) REVERT: c 168 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7693 (mt-10) REVERT: c 171 ASP cc_start: 0.8188 (m-30) cc_final: 0.7806 (m-30) REVERT: c 176 GLN cc_start: 0.8911 (mt0) cc_final: 0.8556 (mt0) REVERT: c 178 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7586 (ttm170) outliers start: 1 outliers final: 0 residues processed: 764 average time/residue: 0.3226 time to fit residues: 347.3143 Evaluate side-chains 741 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 740 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 ASN M 376 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 26 GLN m 54 HIS c 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112898 restraints weight = 30833.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117158 restraints weight = 16821.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120117 restraints weight = 10574.715| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16108 Z= 0.229 Angle : 0.600 7.391 21822 Z= 0.318 Chirality : 0.046 0.181 2524 Planarity : 0.004 0.050 2752 Dihedral : 10.181 168.593 2154 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 1.11 (0.20), residues: 1954 helix: 1.12 (0.18), residues: 814 sheet: 0.15 (0.27), residues: 370 loop : 0.86 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP c 172 HIS 0.003 0.001 HIS M 3 PHE 0.028 0.002 PHE C 51 TYR 0.033 0.002 TYR M 110 ARG 0.005 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 1.742 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8209 (mttt) cc_final: 0.7580 (mmmt) REVERT: B 47 LEU cc_start: 0.9048 (mt) cc_final: 0.8676 (mt) REVERT: B 50 MET cc_start: 0.8697 (mtm) cc_final: 0.8229 (mtm) REVERT: B 51 LEU cc_start: 0.8817 (mt) cc_final: 0.8588 (mt) REVERT: B 52 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 54 ASN cc_start: 0.7929 (m110) cc_final: 0.7649 (m110) REVERT: B 59 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8484 (mttp) REVERT: B 66 ILE cc_start: 0.8595 (mm) cc_final: 0.8259 (mm) REVERT: B 72 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8667 (ttmt) REVERT: B 74 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8192 (mmtt) REVERT: B 79 LEU cc_start: 0.8568 (mt) cc_final: 0.8350 (mt) REVERT: B 80 PHE cc_start: 0.8592 (t80) cc_final: 0.7904 (t80) REVERT: B 83 VAL cc_start: 0.8355 (t) cc_final: 0.8051 (m) REVERT: B 85 LYS cc_start: 0.8554 (mttt) cc_final: 0.7776 (mttt) REVERT: B 90 LYS cc_start: 0.8527 (mttt) cc_final: 0.7735 (mmmm) REVERT: B 101 TYR cc_start: 0.8453 (t80) cc_final: 0.8127 (t80) REVERT: B 112 LEU cc_start: 0.8301 (mp) cc_final: 0.7500 (mp) REVERT: B 121 GLN cc_start: 0.8376 (tt0) cc_final: 0.8134 (tt0) REVERT: B 125 LYS cc_start: 0.8883 (mttt) cc_final: 0.8418 (mtpp) REVERT: B 128 ASN cc_start: 0.8244 (t0) cc_final: 0.7931 (t160) REVERT: B 137 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7217 (mtp-110) REVERT: B 147 ILE cc_start: 0.8460 (pt) cc_final: 0.7570 (pt) REVERT: B 150 ILE cc_start: 0.8504 (mp) cc_final: 0.8256 (tp) REVERT: B 151 MET cc_start: 0.7832 (mtp) cc_final: 0.7168 (mtp) REVERT: B 155 ILE cc_start: 0.9268 (mm) cc_final: 0.9003 (mm) REVERT: B 169 ASN cc_start: 0.8733 (m-40) cc_final: 0.8273 (t0) REVERT: B 175 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 183 GLU cc_start: 0.8580 (mp0) cc_final: 0.8191 (mp0) REVERT: B 186 GLU cc_start: 0.8504 (pm20) cc_final: 0.8034 (pm20) REVERT: B 193 GLU cc_start: 0.8454 (tt0) cc_final: 0.8189 (tt0) REVERT: B 199 LYS cc_start: 0.8038 (mppt) cc_final: 0.7794 (mmtm) REVERT: B 202 LEU cc_start: 0.7690 (mm) cc_final: 0.7261 (tp) REVERT: B 207 VAL cc_start: 0.8790 (t) cc_final: 0.8500 (p) REVERT: B 213 GLU cc_start: 0.8110 (tt0) cc_final: 0.7710 (tt0) REVERT: B 228 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8123 (ttpt) REVERT: B 244 ILE cc_start: 0.9025 (mt) cc_final: 0.8651 (tp) REVERT: B 246 HIS cc_start: 0.8439 (m-70) cc_final: 0.8222 (m-70) REVERT: B 247 MET cc_start: 0.7271 (tmm) cc_final: 0.6786 (tmm) REVERT: B 305 LYS cc_start: 0.8710 (tttt) cc_final: 0.8297 (ttpp) REVERT: B 307 LEU cc_start: 0.8720 (mm) cc_final: 0.8234 (tp) REVERT: B 308 LEU cc_start: 0.8626 (mt) cc_final: 0.8321 (mm) REVERT: B 317 MET cc_start: 0.8599 (tpp) cc_final: 0.8187 (tpp) REVERT: B 321 GLN cc_start: 0.8081 (tt0) cc_final: 0.7604 (tt0) REVERT: B 324 TRP cc_start: 0.8759 (t-100) cc_final: 0.8375 (t-100) REVERT: B 326 ILE cc_start: 0.8032 (mm) cc_final: 0.7763 (mm) REVERT: B 341 ARG cc_start: 0.8714 (ptt90) cc_final: 0.8268 (ptm-80) REVERT: B 346 ASN cc_start: 0.7215 (p0) cc_final: 0.6643 (p0) REVERT: B 360 MET cc_start: 0.8435 (tpp) cc_final: 0.7092 (tpp) REVERT: B 367 MET cc_start: 0.7254 (mtp) cc_final: 0.7048 (mtp) REVERT: B 387 THR cc_start: 0.8242 (m) cc_final: 0.7780 (m) REVERT: B 391 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 417 ASP cc_start: 0.8440 (m-30) cc_final: 0.8123 (m-30) REVERT: M 29 CYS cc_start: 0.8690 (t) cc_final: 0.8204 (t) REVERT: M 34 GLU cc_start: 0.9039 (tt0) cc_final: 0.8661 (tt0) REVERT: M 43 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7487 (mt-10) REVERT: M 77 LEU cc_start: 0.8606 (mt) cc_final: 0.8248 (mt) REVERT: M 78 PHE cc_start: 0.8735 (t80) cc_final: 0.8503 (t80) REVERT: M 88 ASP cc_start: 0.8594 (m-30) cc_final: 0.8262 (m-30) REVERT: M 89 THR cc_start: 0.9042 (m) cc_final: 0.8812 (p) REVERT: M 116 MET cc_start: 0.7909 (mtm) cc_final: 0.7637 (mtm) REVERT: M 123 LEU cc_start: 0.8634 (tp) cc_final: 0.8426 (tp) REVERT: M 125 THR cc_start: 0.8799 (p) cc_final: 0.8409 (t) REVERT: M 126 GLU cc_start: 0.8224 (tp30) cc_final: 0.7792 (tp30) REVERT: M 131 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8141 (mttp) REVERT: M 135 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8464 (mmtt) REVERT: M 157 LEU cc_start: 0.8409 (mt) cc_final: 0.8139 (mt) REVERT: M 161 GLN cc_start: 0.8388 (tp40) cc_final: 0.8161 (tp-100) REVERT: M 203 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6911 (mm-40) REVERT: M 209 CYS cc_start: 0.7464 (t) cc_final: 0.6518 (m) REVERT: M 220 LEU cc_start: 0.8317 (mm) cc_final: 0.7967 (mm) REVERT: M 234 HIS cc_start: 0.8079 (t-90) cc_final: 0.7865 (t-90) REVERT: M 242 TRP cc_start: 0.7726 (t-100) cc_final: 0.7305 (t-100) REVERT: M 245 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6353 (mm-30) REVERT: M 257 PHE cc_start: 0.8396 (p90) cc_final: 0.8179 (p90) REVERT: M 258 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7919 (mtm180) REVERT: M 262 TYR cc_start: 0.8414 (p90) cc_final: 0.8057 (p90) REVERT: M 298 LYS cc_start: 0.9041 (tttt) cc_final: 0.8648 (tttt) REVERT: M 300 ASN cc_start: 0.9072 (p0) cc_final: 0.8862 (p0) REVERT: M 377 PHE cc_start: 0.7881 (p90) cc_final: 0.7550 (p90) REVERT: M 378 LYS cc_start: 0.7817 (pttt) cc_final: 0.7608 (ptmm) REVERT: M 393 ASP cc_start: 0.7993 (t0) cc_final: 0.7596 (t0) REVERT: M 402 PHE cc_start: 0.7718 (m-80) cc_final: 0.7136 (m-80) REVERT: M 414 PHE cc_start: 0.7811 (t80) cc_final: 0.7282 (t80) REVERT: C 23 VAL cc_start: 0.8750 (m) cc_final: 0.8337 (m) REVERT: C 44 THR cc_start: 0.9138 (m) cc_final: 0.8736 (p) REVERT: C 68 VAL cc_start: 0.8219 (t) cc_final: 0.7946 (p) REVERT: C 78 TRP cc_start: 0.8366 (m-10) cc_final: 0.8106 (m-10) REVERT: C 81 TYR cc_start: 0.7177 (m-80) cc_final: 0.6551 (m-80) REVERT: C 82 PHE cc_start: 0.8181 (m-80) cc_final: 0.7337 (m-80) REVERT: C 84 ASN cc_start: 0.8583 (t0) cc_final: 0.7885 (t0) REVERT: C 95 ASN cc_start: 0.7806 (t0) cc_final: 0.7512 (t0) REVERT: C 110 MET cc_start: 0.8578 (mmm) cc_final: 0.8216 (mmm) REVERT: C 115 GLU cc_start: 0.7858 (tt0) cc_final: 0.7607 (tt0) REVERT: C 116 LEU cc_start: 0.8097 (mt) cc_final: 0.7797 (mt) REVERT: C 142 LYS cc_start: 0.8970 (mttm) cc_final: 0.8730 (mttm) REVERT: C 168 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 171 ASP cc_start: 0.8168 (m-30) cc_final: 0.7808 (m-30) REVERT: C 172 TRP cc_start: 0.8261 (t60) cc_final: 0.7994 (t60) REVERT: b 43 LYS cc_start: 0.8205 (mttt) cc_final: 0.7750 (tttp) REVERT: b 47 LEU cc_start: 0.8976 (mt) cc_final: 0.8572 (mt) REVERT: b 48 LYS cc_start: 0.8888 (ptpp) cc_final: 0.8221 (ptpp) REVERT: b 50 MET cc_start: 0.8513 (mtm) cc_final: 0.8121 (mtm) REVERT: b 51 LEU cc_start: 0.8882 (mt) cc_final: 0.8520 (mt) REVERT: b 54 ASN cc_start: 0.7920 (m110) cc_final: 0.7601 (m110) REVERT: b 66 ILE cc_start: 0.8384 (mp) cc_final: 0.8098 (mp) REVERT: b 72 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8281 (mtmt) REVERT: b 80 PHE cc_start: 0.8580 (t80) cc_final: 0.7950 (t80) REVERT: b 101 TYR cc_start: 0.8805 (t80) cc_final: 0.8576 (t80) REVERT: b 107 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7612 (mt-10) REVERT: b 112 LEU cc_start: 0.8137 (mp) cc_final: 0.7362 (mp) REVERT: b 128 ASN cc_start: 0.8135 (t0) cc_final: 0.7742 (t0) REVERT: b 132 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8170 (mtm180) REVERT: b 142 ILE cc_start: 0.9119 (mm) cc_final: 0.8841 (mp) REVERT: b 147 ILE cc_start: 0.8444 (pt) cc_final: 0.7704 (pt) REVERT: b 150 ILE cc_start: 0.8276 (mt) cc_final: 0.7981 (mt) REVERT: b 151 MET cc_start: 0.7604 (mtp) cc_final: 0.6945 (mtp) REVERT: b 162 LEU cc_start: 0.8016 (mp) cc_final: 0.7192 (tp) REVERT: b 181 ASP cc_start: 0.8372 (t0) cc_final: 0.7962 (t0) REVERT: b 187 MET cc_start: 0.8257 (mtm) cc_final: 0.7997 (mtm) REVERT: b 190 GLU cc_start: 0.8050 (tt0) cc_final: 0.7769 (tt0) REVERT: b 193 GLU cc_start: 0.8522 (tt0) cc_final: 0.8080 (tt0) REVERT: b 195 LEU cc_start: 0.9088 (mt) cc_final: 0.8747 (mt) REVERT: b 199 LYS cc_start: 0.8117 (mppt) cc_final: 0.7802 (mmtm) REVERT: b 202 LEU cc_start: 0.7860 (mm) cc_final: 0.7421 (tp) REVERT: b 207 VAL cc_start: 0.8849 (t) cc_final: 0.8555 (p) REVERT: b 212 GLU cc_start: 0.8200 (tp30) cc_final: 0.7831 (tp30) REVERT: b 228 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8168 (ttpt) REVERT: b 244 ILE cc_start: 0.9109 (mt) cc_final: 0.8690 (tp) REVERT: b 246 HIS cc_start: 0.8428 (m-70) cc_final: 0.8183 (m-70) REVERT: b 247 MET cc_start: 0.7476 (tmm) cc_final: 0.5802 (tmm) REVERT: b 298 ARG cc_start: 0.8934 (mmm160) cc_final: 0.7392 (mpt180) REVERT: b 307 LEU cc_start: 0.8881 (mt) cc_final: 0.8552 (mt) REVERT: b 308 LEU cc_start: 0.8781 (mt) cc_final: 0.8456 (mm) REVERT: b 311 ARG cc_start: 0.8303 (ptt180) cc_final: 0.7818 (ptt-90) REVERT: b 317 MET cc_start: 0.8655 (tpp) cc_final: 0.8283 (tpp) REVERT: b 321 GLN cc_start: 0.8054 (tt0) cc_final: 0.7461 (tt0) REVERT: b 322 LEU cc_start: 0.8507 (tt) cc_final: 0.8278 (tt) REVERT: b 324 TRP cc_start: 0.8660 (t-100) cc_final: 0.8041 (t-100) REVERT: b 326 ILE cc_start: 0.8078 (mm) cc_final: 0.7781 (mm) REVERT: b 331 GLU cc_start: 0.7109 (mp0) cc_final: 0.6745 (mp0) REVERT: b 341 ARG cc_start: 0.8671 (ptt90) cc_final: 0.8009 (ttp80) REVERT: b 346 ASN cc_start: 0.7380 (p0) cc_final: 0.6966 (p0) REVERT: b 363 GLN cc_start: 0.8855 (mp10) cc_final: 0.8532 (mp10) REVERT: b 367 MET cc_start: 0.7129 (mmp) cc_final: 0.6741 (mmt) REVERT: b 384 MET cc_start: 0.7985 (ptt) cc_final: 0.7442 (ptt) REVERT: b 391 GLU cc_start: 0.8277 (tp30) cc_final: 0.8077 (tp30) REVERT: m 1 MET cc_start: 0.6994 (mtt) cc_final: 0.6632 (mtt) REVERT: m 17 GLU cc_start: 0.7584 (pt0) cc_final: 0.7292 (pt0) REVERT: m 21 LYS cc_start: 0.8017 (mttt) cc_final: 0.7482 (mttm) REVERT: m 29 CYS cc_start: 0.8600 (m) cc_final: 0.7994 (t) REVERT: m 36 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7992 (tp-100) REVERT: m 43 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7571 (mt-10) REVERT: m 44 ASN cc_start: 0.8368 (t0) cc_final: 0.7656 (t0) REVERT: m 45 VAL cc_start: 0.8888 (t) cc_final: 0.8673 (t) REVERT: m 71 GLN cc_start: 0.8322 (tp40) cc_final: 0.7884 (tp40) REVERT: m 77 LEU cc_start: 0.8618 (mt) cc_final: 0.8355 (mt) REVERT: m 78 PHE cc_start: 0.8799 (t80) cc_final: 0.8538 (t80) REVERT: m 80 ILE cc_start: 0.8591 (mt) cc_final: 0.8304 (mm) REVERT: m 88 ASP cc_start: 0.8529 (m-30) cc_final: 0.8155 (m-30) REVERT: m 89 THR cc_start: 0.8943 (m) cc_final: 0.8685 (p) REVERT: m 90 PHE cc_start: 0.8750 (m-10) cc_final: 0.8511 (m-10) REVERT: m 108 ILE cc_start: 0.8945 (mt) cc_final: 0.8557 (mm) REVERT: m 111 GLU cc_start: 0.8079 (tt0) cc_final: 0.7831 (tt0) REVERT: m 116 MET cc_start: 0.7712 (mtm) cc_final: 0.7461 (mtm) REVERT: m 123 LEU cc_start: 0.8454 (tp) cc_final: 0.8199 (tp) REVERT: m 128 ASN cc_start: 0.8306 (m-40) cc_final: 0.8077 (m-40) REVERT: m 129 ILE cc_start: 0.8914 (mm) cc_final: 0.8639 (tp) REVERT: m 134 ILE cc_start: 0.8338 (mt) cc_final: 0.8115 (tp) REVERT: m 140 LEU cc_start: 0.8506 (mt) cc_final: 0.8262 (tt) REVERT: m 141 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7754 (mmt90) REVERT: m 157 LEU cc_start: 0.8509 (mt) cc_final: 0.8247 (pp) REVERT: m 161 GLN cc_start: 0.8323 (tp40) cc_final: 0.7980 (tp-100) REVERT: m 203 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6806 (mm-40) REVERT: m 209 CYS cc_start: 0.7478 (t) cc_final: 0.6532 (m) REVERT: m 220 LEU cc_start: 0.8265 (mm) cc_final: 0.7980 (mm) REVERT: m 234 HIS cc_start: 0.8086 (t-90) cc_final: 0.7689 (t-90) REVERT: m 240 LYS cc_start: 0.8631 (mttt) cc_final: 0.7799 (mmmm) REVERT: m 243 GLU cc_start: 0.8599 (tp30) cc_final: 0.8240 (tp30) REVERT: m 250 PHE cc_start: 0.6878 (p90) cc_final: 0.6633 (p90) REVERT: m 257 PHE cc_start: 0.8491 (p90) cc_final: 0.8204 (p90) REVERT: m 258 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7949 (mtm180) REVERT: m 262 TYR cc_start: 0.8217 (p90) cc_final: 0.6970 (p90) REVERT: m 298 LYS cc_start: 0.9072 (tttt) cc_final: 0.8714 (tttt) REVERT: m 378 LYS cc_start: 0.8031 (pttt) cc_final: 0.7665 (ptmm) REVERT: m 387 LEU cc_start: 0.8724 (tp) cc_final: 0.7867 (pt) REVERT: m 393 ASP cc_start: 0.8090 (t0) cc_final: 0.7695 (t0) REVERT: m 403 LYS cc_start: 0.7735 (mptt) cc_final: 0.7394 (mmtm) REVERT: m 406 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8339 (ttmt) REVERT: m 407 TYR cc_start: 0.8646 (m-80) cc_final: 0.8031 (m-80) REVERT: m 414 PHE cc_start: 0.7882 (t80) cc_final: 0.7492 (t80) REVERT: c 37 LEU cc_start: 0.8923 (mt) cc_final: 0.8719 (mt) REVERT: c 58 TYR cc_start: 0.8296 (t80) cc_final: 0.7162 (t80) REVERT: c 64 THR cc_start: 0.6665 (m) cc_final: 0.6306 (t) REVERT: c 81 TYR cc_start: 0.7271 (m-80) cc_final: 0.6830 (m-80) REVERT: c 82 PHE cc_start: 0.8149 (m-10) cc_final: 0.7884 (m-80) REVERT: c 84 ASN cc_start: 0.8411 (t0) cc_final: 0.7579 (t0) REVERT: c 86 GLN cc_start: 0.7917 (mm-40) cc_final: 0.6860 (mt0) REVERT: c 110 MET cc_start: 0.8517 (mmm) cc_final: 0.7975 (mmm) REVERT: c 115 GLU cc_start: 0.7886 (tt0) cc_final: 0.7623 (tt0) REVERT: c 128 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6863 (mm-40) REVERT: c 135 ASN cc_start: 0.7924 (p0) cc_final: 0.7533 (p0) REVERT: c 167 TYR cc_start: 0.8174 (m-10) cc_final: 0.7347 (m-80) REVERT: c 171 ASP cc_start: 0.8168 (m-30) cc_final: 0.7711 (m-30) REVERT: c 172 TRP cc_start: 0.8177 (t60) cc_final: 0.7460 (t60) REVERT: c 178 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7694 (ttm170) REVERT: y 411 HIS cc_start: 0.5286 (t-90) cc_final: 0.4576 (t-170) REVERT: y 415 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7605 (mm110) outliers start: 0 outliers final: 0 residues processed: 776 average time/residue: 0.3209 time to fit residues: 351.1292 Evaluate side-chains 745 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 55 optimal weight: 0.0470 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 321 GLN ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 ASN m 376 GLN m 380 GLN c 95 ASN ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111256 restraints weight = 30947.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115584 restraints weight = 16912.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118637 restraints weight = 10544.837| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16108 Z= 0.190 Angle : 0.578 7.869 21822 Z= 0.302 Chirality : 0.045 0.205 2524 Planarity : 0.004 0.050 2752 Dihedral : 9.856 166.117 2154 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1954 helix: 1.21 (0.18), residues: 808 sheet: 0.32 (0.27), residues: 374 loop : 0.92 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP c 172 HIS 0.010 0.001 HIS M 3 PHE 0.022 0.001 PHE C 51 TYR 0.024 0.002 TYR B 351 ARG 0.008 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 772 time to evaluate : 1.830 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8166 (mttt) cc_final: 0.7555 (mmmt) REVERT: B 47 LEU cc_start: 0.9045 (mt) cc_final: 0.8664 (mt) REVERT: B 50 MET cc_start: 0.8598 (mtm) cc_final: 0.8155 (mtm) REVERT: B 51 LEU cc_start: 0.8819 (mt) cc_final: 0.8544 (mt) REVERT: B 52 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 54 ASN cc_start: 0.7963 (m110) cc_final: 0.7639 (m110) REVERT: B 55 LYS cc_start: 0.8275 (mtpt) cc_final: 0.8072 (mtpt) REVERT: B 59 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8581 (mttt) REVERT: B 63 MET cc_start: 0.8743 (mmm) cc_final: 0.8100 (mmm) REVERT: B 66 ILE cc_start: 0.8517 (mm) cc_final: 0.8093 (mm) REVERT: B 72 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8666 (ttmt) REVERT: B 74 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8246 (mmtt) REVERT: B 80 PHE cc_start: 0.8579 (t80) cc_final: 0.8018 (t80) REVERT: B 83 VAL cc_start: 0.8310 (t) cc_final: 0.8085 (t) REVERT: B 85 LYS cc_start: 0.8568 (mttt) cc_final: 0.7768 (mttt) REVERT: B 90 LYS cc_start: 0.8527 (mttt) cc_final: 0.7718 (mmmm) REVERT: B 97 LEU cc_start: 0.8626 (mt) cc_final: 0.7991 (mp) REVERT: B 101 TYR cc_start: 0.8591 (t80) cc_final: 0.8367 (t80) REVERT: B 112 LEU cc_start: 0.8334 (mp) cc_final: 0.7518 (mp) REVERT: B 121 GLN cc_start: 0.8352 (tt0) cc_final: 0.8099 (tt0) REVERT: B 125 LYS cc_start: 0.8889 (mttt) cc_final: 0.8445 (mtpp) REVERT: B 128 ASN cc_start: 0.8057 (t0) cc_final: 0.7804 (t0) REVERT: B 132 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: B 137 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7221 (mtp-110) REVERT: B 147 ILE cc_start: 0.8405 (pt) cc_final: 0.7546 (pt) REVERT: B 150 ILE cc_start: 0.8497 (mp) cc_final: 0.8232 (tp) REVERT: B 151 MET cc_start: 0.7789 (mtp) cc_final: 0.7119 (mtp) REVERT: B 155 ILE cc_start: 0.9236 (mm) cc_final: 0.8905 (mm) REVERT: B 169 ASN cc_start: 0.8710 (m-40) cc_final: 0.8236 (t0) REVERT: B 175 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 181 ASP cc_start: 0.8487 (t0) cc_final: 0.7972 (t0) REVERT: B 183 GLU cc_start: 0.8510 (mp0) cc_final: 0.8249 (mp0) REVERT: B 186 GLU cc_start: 0.8340 (pm20) cc_final: 0.7979 (pm20) REVERT: B 190 GLU cc_start: 0.8109 (tt0) cc_final: 0.7786 (tt0) REVERT: B 193 GLU cc_start: 0.8510 (tt0) cc_final: 0.8063 (tt0) REVERT: B 199 LYS cc_start: 0.8027 (mppt) cc_final: 0.7819 (mmtm) REVERT: B 202 LEU cc_start: 0.7684 (mm) cc_final: 0.7191 (tp) REVERT: B 207 VAL cc_start: 0.8739 (t) cc_final: 0.8472 (p) REVERT: B 213 GLU cc_start: 0.8068 (tt0) cc_final: 0.7726 (tt0) REVERT: B 215 CYS cc_start: 0.8878 (m) cc_final: 0.8241 (p) REVERT: B 228 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8095 (ttpt) REVERT: B 244 ILE cc_start: 0.8970 (mt) cc_final: 0.8578 (tp) REVERT: B 247 MET cc_start: 0.7210 (tmm) cc_final: 0.6661 (tmm) REVERT: B 305 LYS cc_start: 0.8620 (tttt) cc_final: 0.8369 (tttp) REVERT: B 308 LEU cc_start: 0.8600 (mt) cc_final: 0.8268 (mm) REVERT: B 311 ARG cc_start: 0.8102 (ptt180) cc_final: 0.7535 (ptt90) REVERT: B 317 MET cc_start: 0.8583 (tpp) cc_final: 0.8214 (tpp) REVERT: B 321 GLN cc_start: 0.8063 (tt0) cc_final: 0.7555 (tt0) REVERT: B 322 LEU cc_start: 0.8389 (tt) cc_final: 0.8170 (tt) REVERT: B 324 TRP cc_start: 0.8767 (t-100) cc_final: 0.8370 (t-100) REVERT: B 326 ILE cc_start: 0.7980 (mm) cc_final: 0.7644 (mm) REVERT: B 341 ARG cc_start: 0.8713 (ptt90) cc_final: 0.8248 (ptm-80) REVERT: B 346 ASN cc_start: 0.7163 (p0) cc_final: 0.6650 (p0) REVERT: B 351 TYR cc_start: 0.8077 (t80) cc_final: 0.7270 (t80) REVERT: B 355 GLN cc_start: 0.8721 (mt0) cc_final: 0.8427 (mt0) REVERT: B 360 MET cc_start: 0.8595 (tpp) cc_final: 0.7099 (tpp) REVERT: B 367 MET cc_start: 0.7180 (mtp) cc_final: 0.6969 (mtp) REVERT: B 387 THR cc_start: 0.8218 (m) cc_final: 0.7780 (m) REVERT: B 388 LEU cc_start: 0.8786 (mt) cc_final: 0.8298 (mm) REVERT: B 391 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7117 (mt-10) REVERT: B 417 ASP cc_start: 0.8447 (m-30) cc_final: 0.8154 (m-30) REVERT: B 631 THR cc_start: 0.8762 (m) cc_final: 0.8540 (t) REVERT: M 17 GLU cc_start: 0.7583 (pt0) cc_final: 0.7362 (pt0) REVERT: M 29 CYS cc_start: 0.8667 (t) cc_final: 0.8193 (t) REVERT: M 31 TYR cc_start: 0.8229 (m-80) cc_final: 0.7895 (m-10) REVERT: M 34 GLU cc_start: 0.9003 (tt0) cc_final: 0.8674 (tt0) REVERT: M 41 ASP cc_start: 0.8465 (t0) cc_final: 0.8212 (t0) REVERT: M 43 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7469 (mt-10) REVERT: M 71 GLN cc_start: 0.8204 (mm110) cc_final: 0.7914 (mm-40) REVERT: M 77 LEU cc_start: 0.8502 (mt) cc_final: 0.8137 (mt) REVERT: M 78 PHE cc_start: 0.8690 (t80) cc_final: 0.8473 (t80) REVERT: M 88 ASP cc_start: 0.8581 (m-30) cc_final: 0.8226 (m-30) REVERT: M 89 THR cc_start: 0.9151 (m) cc_final: 0.8830 (p) REVERT: M 116 MET cc_start: 0.7988 (mtm) cc_final: 0.7692 (mtm) REVERT: M 123 LEU cc_start: 0.8612 (tp) cc_final: 0.8275 (tp) REVERT: M 126 GLU cc_start: 0.8288 (tp30) cc_final: 0.7626 (tp30) REVERT: M 128 ASN cc_start: 0.8414 (m-40) cc_final: 0.7933 (m-40) REVERT: M 130 LEU cc_start: 0.8421 (tp) cc_final: 0.8018 (tp) REVERT: M 131 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8210 (mttp) REVERT: M 135 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8405 (mmtt) REVERT: M 157 LEU cc_start: 0.8448 (mt) cc_final: 0.8233 (pp) REVERT: M 161 GLN cc_start: 0.8382 (tp40) cc_final: 0.8102 (tp-100) REVERT: M 209 CYS cc_start: 0.7298 (t) cc_final: 0.6457 (m) REVERT: M 220 LEU cc_start: 0.8204 (mm) cc_final: 0.7793 (mm) REVERT: M 234 HIS cc_start: 0.8074 (t-90) cc_final: 0.7738 (t-90) REVERT: M 242 TRP cc_start: 0.7727 (t-100) cc_final: 0.7260 (t-100) REVERT: M 245 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6222 (mm-30) REVERT: M 258 ARG cc_start: 0.8329 (mtm180) cc_final: 0.7898 (mtm180) REVERT: M 262 TYR cc_start: 0.8375 (p90) cc_final: 0.8021 (p90) REVERT: M 298 LYS cc_start: 0.9050 (tttt) cc_final: 0.8653 (tttt) REVERT: M 377 PHE cc_start: 0.7857 (p90) cc_final: 0.7580 (p90) REVERT: M 393 ASP cc_start: 0.7814 (t0) cc_final: 0.7493 (t0) REVERT: M 414 PHE cc_start: 0.7803 (t80) cc_final: 0.7174 (t80) REVERT: C 23 VAL cc_start: 0.8778 (m) cc_final: 0.8403 (m) REVERT: C 44 THR cc_start: 0.9131 (m) cc_final: 0.8724 (p) REVERT: C 68 VAL cc_start: 0.8198 (t) cc_final: 0.7920 (p) REVERT: C 78 TRP cc_start: 0.8328 (m-10) cc_final: 0.7918 (m-10) REVERT: C 81 TYR cc_start: 0.7167 (m-80) cc_final: 0.6443 (m-80) REVERT: C 82 PHE cc_start: 0.8182 (m-80) cc_final: 0.7328 (m-80) REVERT: C 84 ASN cc_start: 0.8579 (t0) cc_final: 0.7903 (t0) REVERT: C 95 ASN cc_start: 0.7793 (t0) cc_final: 0.7464 (t0) REVERT: C 110 MET cc_start: 0.8563 (mmm) cc_final: 0.8112 (mmm) REVERT: C 115 GLU cc_start: 0.7918 (tt0) cc_final: 0.7565 (tt0) REVERT: C 117 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8253 (ttp-110) REVERT: C 142 LYS cc_start: 0.8967 (mttm) cc_final: 0.8737 (mttm) REVERT: C 168 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 171 ASP cc_start: 0.7990 (m-30) cc_final: 0.7788 (m-30) REVERT: b 43 LYS cc_start: 0.8139 (mttt) cc_final: 0.7692 (tptm) REVERT: b 47 LEU cc_start: 0.9028 (mt) cc_final: 0.8544 (mt) REVERT: b 50 MET cc_start: 0.8493 (mtm) cc_final: 0.8117 (mtm) REVERT: b 51 LEU cc_start: 0.8831 (mt) cc_final: 0.8479 (mt) REVERT: b 54 ASN cc_start: 0.7940 (m110) cc_final: 0.7709 (m110) REVERT: b 63 MET cc_start: 0.8644 (mmm) cc_final: 0.8067 (mmm) REVERT: b 80 PHE cc_start: 0.8470 (t80) cc_final: 0.7941 (t80) REVERT: b 107 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7537 (mt-10) REVERT: b 112 LEU cc_start: 0.8140 (mp) cc_final: 0.7361 (mp) REVERT: b 121 GLN cc_start: 0.8181 (tt0) cc_final: 0.7902 (mt0) REVERT: b 130 LEU cc_start: 0.8463 (tp) cc_final: 0.8262 (tp) REVERT: b 132 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8130 (mtm180) REVERT: b 147 ILE cc_start: 0.8391 (pt) cc_final: 0.7682 (pt) REVERT: b 150 ILE cc_start: 0.8280 (mt) cc_final: 0.7994 (mt) REVERT: b 151 MET cc_start: 0.7585 (mtp) cc_final: 0.6939 (mtp) REVERT: b 162 LEU cc_start: 0.7999 (mp) cc_final: 0.7129 (tp) REVERT: b 190 GLU cc_start: 0.8051 (tt0) cc_final: 0.7770 (tt0) REVERT: b 195 LEU cc_start: 0.9056 (mt) cc_final: 0.8701 (mt) REVERT: b 199 LYS cc_start: 0.8090 (mppt) cc_final: 0.7845 (mmtm) REVERT: b 202 LEU cc_start: 0.7746 (mm) cc_final: 0.7277 (tp) REVERT: b 207 VAL cc_start: 0.8788 (t) cc_final: 0.8497 (p) REVERT: b 212 GLU cc_start: 0.8224 (tp30) cc_final: 0.7710 (tp30) REVERT: b 215 CYS cc_start: 0.8913 (m) cc_final: 0.8352 (p) REVERT: b 228 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8204 (ttpt) REVERT: b 237 GLU cc_start: 0.7684 (tt0) cc_final: 0.7172 (tt0) REVERT: b 241 GLN cc_start: 0.8169 (mt0) cc_final: 0.7517 (mt0) REVERT: b 244 ILE cc_start: 0.9107 (mt) cc_final: 0.8682 (tp) REVERT: b 247 MET cc_start: 0.7282 (tmm) cc_final: 0.6723 (tmm) REVERT: b 307 LEU cc_start: 0.8892 (mt) cc_final: 0.8549 (mt) REVERT: b 308 LEU cc_start: 0.8764 (mt) cc_final: 0.8448 (mm) REVERT: b 311 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7692 (ptt-90) REVERT: b 317 MET cc_start: 0.8599 (tpp) cc_final: 0.8267 (tpp) REVERT: b 321 GLN cc_start: 0.7991 (tt0) cc_final: 0.7470 (tt0) REVERT: b 324 TRP cc_start: 0.8741 (t-100) cc_final: 0.8180 (t-100) REVERT: b 326 ILE cc_start: 0.8021 (mm) cc_final: 0.7759 (mm) REVERT: b 331 GLU cc_start: 0.7201 (mp0) cc_final: 0.6775 (mp0) REVERT: b 341 ARG cc_start: 0.8656 (ptt90) cc_final: 0.7993 (ttp80) REVERT: b 346 ASN cc_start: 0.7324 (p0) cc_final: 0.6916 (p0) REVERT: b 352 ILE cc_start: 0.8597 (mm) cc_final: 0.8377 (mm) REVERT: b 363 GLN cc_start: 0.8858 (mp10) cc_final: 0.8541 (mp10) REVERT: b 367 MET cc_start: 0.7304 (mmp) cc_final: 0.6981 (mmt) REVERT: b 384 MET cc_start: 0.7914 (ptt) cc_final: 0.7402 (ptt) REVERT: b 391 GLU cc_start: 0.8261 (tp30) cc_final: 0.8043 (tp30) REVERT: b 629 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8059 (ttmt) REVERT: m 1 MET cc_start: 0.6974 (mtt) cc_final: 0.6665 (mtt) REVERT: m 17 GLU cc_start: 0.7528 (pt0) cc_final: 0.7229 (pt0) REVERT: m 21 LYS cc_start: 0.7993 (mttt) cc_final: 0.7502 (mttm) REVERT: m 29 CYS cc_start: 0.8564 (m) cc_final: 0.7925 (t) REVERT: m 36 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7990 (tp-100) REVERT: m 43 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7582 (mt-10) REVERT: m 44 ASN cc_start: 0.8367 (t0) cc_final: 0.7597 (t0) REVERT: m 45 VAL cc_start: 0.8877 (t) cc_final: 0.8664 (t) REVERT: m 71 GLN cc_start: 0.8294 (tp40) cc_final: 0.7976 (tp40) REVERT: m 74 VAL cc_start: 0.9000 (t) cc_final: 0.8731 (t) REVERT: m 78 PHE cc_start: 0.8775 (t80) cc_final: 0.8570 (t80) REVERT: m 80 ILE cc_start: 0.8567 (mt) cc_final: 0.8292 (mm) REVERT: m 88 ASP cc_start: 0.8462 (m-30) cc_final: 0.8139 (m-30) REVERT: m 89 THR cc_start: 0.8965 (m) cc_final: 0.8625 (p) REVERT: m 111 GLU cc_start: 0.8007 (tt0) cc_final: 0.7677 (tt0) REVERT: m 116 MET cc_start: 0.7736 (mtm) cc_final: 0.7390 (mtm) REVERT: m 123 LEU cc_start: 0.8476 (tp) cc_final: 0.8201 (tp) REVERT: m 126 GLU cc_start: 0.8330 (tp30) cc_final: 0.7524 (tp30) REVERT: m 128 ASN cc_start: 0.8290 (m-40) cc_final: 0.7605 (m-40) REVERT: m 129 ILE cc_start: 0.8921 (mm) cc_final: 0.8603 (tp) REVERT: m 134 ILE cc_start: 0.8285 (mt) cc_final: 0.7702 (tp) REVERT: m 140 LEU cc_start: 0.8480 (mt) cc_final: 0.8241 (tt) REVERT: m 141 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7699 (mmt90) REVERT: m 157 LEU cc_start: 0.8477 (mt) cc_final: 0.8202 (pp) REVERT: m 161 GLN cc_start: 0.8310 (tp40) cc_final: 0.7986 (tp-100) REVERT: m 209 CYS cc_start: 0.7500 (t) cc_final: 0.6427 (m) REVERT: m 220 LEU cc_start: 0.8119 (mm) cc_final: 0.7801 (mm) REVERT: m 234 HIS cc_start: 0.8069 (t-90) cc_final: 0.7705 (t-90) REVERT: m 240 LYS cc_start: 0.8577 (mttt) cc_final: 0.8047 (mmmm) REVERT: m 243 GLU cc_start: 0.8610 (tp30) cc_final: 0.8249 (tp30) REVERT: m 257 PHE cc_start: 0.8506 (p90) cc_final: 0.8181 (p90) REVERT: m 258 ARG cc_start: 0.8416 (mtm180) cc_final: 0.7967 (mtm180) REVERT: m 262 TYR cc_start: 0.8191 (p90) cc_final: 0.6972 (p90) REVERT: m 298 LYS cc_start: 0.9076 (tttt) cc_final: 0.8708 (tttt) REVERT: m 377 PHE cc_start: 0.7659 (p90) cc_final: 0.7443 (p90) REVERT: m 378 LYS cc_start: 0.8057 (pttt) cc_final: 0.7656 (ptmm) REVERT: m 387 LEU cc_start: 0.8717 (tp) cc_final: 0.7862 (pt) REVERT: m 393 ASP cc_start: 0.7985 (t0) cc_final: 0.7620 (t0) REVERT: m 400 LYS cc_start: 0.8912 (mmtm) cc_final: 0.8676 (mmtt) REVERT: m 403 LYS cc_start: 0.7643 (mptt) cc_final: 0.7303 (mmtm) REVERT: m 406 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8362 (ttmt) REVERT: m 407 TYR cc_start: 0.8613 (m-80) cc_final: 0.8073 (m-80) REVERT: m 414 PHE cc_start: 0.7858 (t80) cc_final: 0.7537 (t80) REVERT: c 53 VAL cc_start: 0.8646 (t) cc_final: 0.8431 (m) REVERT: c 58 TYR cc_start: 0.8228 (t80) cc_final: 0.7089 (t80) REVERT: c 64 THR cc_start: 0.6564 (m) cc_final: 0.6181 (t) REVERT: c 78 TRP cc_start: 0.8361 (m-10) cc_final: 0.7459 (m-10) REVERT: c 84 ASN cc_start: 0.8433 (t0) cc_final: 0.7635 (t0) REVERT: c 110 MET cc_start: 0.8504 (mmm) cc_final: 0.7972 (mmm) REVERT: c 115 GLU cc_start: 0.7867 (tt0) cc_final: 0.7547 (tt0) REVERT: c 128 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6789 (mm-40) REVERT: c 132 ASN cc_start: 0.8416 (m-40) cc_final: 0.7996 (m-40) REVERT: c 145 LEU cc_start: 0.8263 (mt) cc_final: 0.7994 (mt) REVERT: c 167 TYR cc_start: 0.8181 (m-10) cc_final: 0.7155 (m-80) REVERT: c 171 ASP cc_start: 0.8115 (m-30) cc_final: 0.7763 (m-30) REVERT: c 178 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7633 (ttm170) REVERT: y 415 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7611 (mm110) outliers start: 1 outliers final: 1 residues processed: 772 average time/residue: 0.3203 time to fit residues: 348.6896 Evaluate side-chains 747 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 746 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 158 optimal weight: 0.1980 chunk 141 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN B 303 ASN B 355 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 411 HIS b 321 GLN m 203 GLN c 95 ASN ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 411 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111960 restraints weight = 30669.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116331 restraints weight = 16648.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119334 restraints weight = 10365.592| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16108 Z= 0.187 Angle : 0.575 8.209 21822 Z= 0.302 Chirality : 0.045 0.172 2524 Planarity : 0.004 0.045 2752 Dihedral : 9.582 164.035 2154 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.43 % 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: 1.22 (0.20), residues: 1954 helix: 1.21 (0.18), residues: 816 sheet: 0.28 (0.27), residues: 390 loop : 0.91 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP c 172 HIS 0.014 0.001 HIS M 3 PHE 0.026 0.002 PHE m 121 TYR 0.021 0.002 TYR C 58 ARG 0.009 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 767 time to evaluate : 1.866 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: symmetry clash REVERT: B 43 LYS cc_start: 0.8166 (mttt) cc_final: 0.7563 (tptt) REVERT: B 47 LEU cc_start: 0.9078 (mt) cc_final: 0.8676 (mt) REVERT: B 50 MET cc_start: 0.8649 (mtm) cc_final: 0.8198 (mtm) REVERT: B 51 LEU cc_start: 0.8827 (mt) cc_final: 0.8500 (mt) REVERT: B 52 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 63 MET cc_start: 0.8765 (mmm) cc_final: 0.8230 (mmm) REVERT: B 66 ILE cc_start: 0.8567 (mm) cc_final: 0.8182 (mm) REVERT: B 72 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8561 (ttmt) REVERT: B 74 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8117 (mmtt) REVERT: B 80 PHE cc_start: 0.8574 (t80) cc_final: 0.7996 (t80) REVERT: B 83 VAL cc_start: 0.8311 (t) cc_final: 0.8060 (t) REVERT: B 85 LYS cc_start: 0.8589 (mttt) cc_final: 0.7780 (mttt) REVERT: B 90 LYS cc_start: 0.8528 (mttt) cc_final: 0.7723 (mmmm) REVERT: B 97 LEU cc_start: 0.8594 (mt) cc_final: 0.8108 (mt) REVERT: B 101 TYR cc_start: 0.8520 (t80) cc_final: 0.8272 (t80) REVERT: B 107 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 112 LEU cc_start: 0.8278 (mp) cc_final: 0.7478 (mp) REVERT: B 121 GLN cc_start: 0.8385 (tt0) cc_final: 0.8076 (tt0) REVERT: B 125 LYS cc_start: 0.8899 (mttt) cc_final: 0.8452 (mtpp) REVERT: B 132 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8286 (mtm-85) REVERT: B 137 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7385 (mtp-110) REVERT: B 141 SER cc_start: 0.8657 (m) cc_final: 0.8202 (p) REVERT: B 147 ILE cc_start: 0.8331 (pt) cc_final: 0.7417 (pt) REVERT: B 150 ILE cc_start: 0.8459 (mp) cc_final: 0.8223 (tp) REVERT: B 151 MET cc_start: 0.7775 (mtp) cc_final: 0.7109 (mtp) REVERT: B 155 ILE cc_start: 0.9235 (mm) cc_final: 0.8918 (mm) REVERT: B 175 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 183 GLU cc_start: 0.8504 (mp0) cc_final: 0.8112 (mp0) REVERT: B 186 GLU cc_start: 0.8273 (pm20) cc_final: 0.7974 (pm20) REVERT: B 190 GLU cc_start: 0.8129 (tt0) cc_final: 0.7785 (tt0) REVERT: B 193 GLU cc_start: 0.8512 (tt0) cc_final: 0.8074 (tt0) REVERT: B 199 LYS cc_start: 0.8005 (mppt) cc_final: 0.7776 (mmtm) REVERT: B 202 LEU cc_start: 0.7506 (mm) cc_final: 0.7051 (tp) REVERT: B 207 VAL cc_start: 0.8574 (t) cc_final: 0.8277 (p) REVERT: B 213 GLU cc_start: 0.7957 (tt0) cc_final: 0.7705 (tt0) REVERT: B 215 CYS cc_start: 0.8918 (m) cc_final: 0.8497 (p) REVERT: B 221 LEU cc_start: 0.9151 (mt) cc_final: 0.8824 (mt) REVERT: B 228 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8122 (ttpt) REVERT: B 237 GLU cc_start: 0.7808 (tt0) cc_final: 0.7498 (tt0) REVERT: B 241 GLN cc_start: 0.8176 (mt0) cc_final: 0.7514 (mt0) REVERT: B 244 ILE cc_start: 0.9008 (mt) cc_final: 0.8608 (tp) REVERT: B 247 MET cc_start: 0.7201 (tmm) cc_final: 0.6622 (tmm) REVERT: B 308 LEU cc_start: 0.8668 (mt) cc_final: 0.8295 (mm) REVERT: B 311 ARG cc_start: 0.8080 (ptt180) cc_final: 0.7540 (ptt90) REVERT: B 317 MET cc_start: 0.8568 (tpp) cc_final: 0.8240 (tpp) REVERT: B 321 GLN cc_start: 0.8114 (tt0) cc_final: 0.7403 (tt0) REVERT: B 322 LEU cc_start: 0.8382 (tt) cc_final: 0.8097 (tt) REVERT: B 324 TRP cc_start: 0.8754 (t-100) cc_final: 0.8294 (t-100) REVERT: B 326 ILE cc_start: 0.7923 (mm) cc_final: 0.7609 (mm) REVERT: B 341 ARG cc_start: 0.8708 (ptt90) cc_final: 0.8236 (ptm-80) REVERT: B 346 ASN cc_start: 0.7123 (p0) cc_final: 0.6203 (p0) REVERT: B 348 GLU cc_start: 0.8111 (mp0) cc_final: 0.7770 (mp0) REVERT: B 360 MET cc_start: 0.8581 (tpp) cc_final: 0.6975 (tpp) REVERT: B 384 MET cc_start: 0.8095 (ptt) cc_final: 0.7788 (ptt) REVERT: B 387 THR cc_start: 0.8178 (m) cc_final: 0.7732 (m) REVERT: B 388 LEU cc_start: 0.8796 (mt) cc_final: 0.8241 (mm) REVERT: B 391 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7092 (mt-10) REVERT: B 417 ASP cc_start: 0.8459 (m-30) cc_final: 0.8167 (m-30) REVERT: M 17 GLU cc_start: 0.7539 (pt0) cc_final: 0.7184 (pt0) REVERT: M 26 GLN cc_start: 0.8373 (mt0) cc_final: 0.8038 (tt0) REVERT: M 29 CYS cc_start: 0.8719 (t) cc_final: 0.8192 (t) REVERT: M 31 TYR cc_start: 0.8243 (m-80) cc_final: 0.7918 (m-10) REVERT: M 34 GLU cc_start: 0.9001 (tt0) cc_final: 0.8661 (tt0) REVERT: M 41 ASP cc_start: 0.8494 (t0) cc_final: 0.8221 (t0) REVERT: M 43 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7533 (mt-10) REVERT: M 63 LYS cc_start: 0.8343 (mttt) cc_final: 0.7565 (tmtt) REVERT: M 71 GLN cc_start: 0.8135 (mm110) cc_final: 0.7917 (mm-40) REVERT: M 77 LEU cc_start: 0.8543 (mt) cc_final: 0.8187 (mt) REVERT: M 78 PHE cc_start: 0.8711 (t80) cc_final: 0.8497 (t80) REVERT: M 88 ASP cc_start: 0.8533 (m-30) cc_final: 0.8185 (m-30) REVERT: M 89 THR cc_start: 0.9162 (m) cc_final: 0.8865 (p) REVERT: M 116 MET cc_start: 0.8012 (mtm) cc_final: 0.7784 (mtm) REVERT: M 126 GLU cc_start: 0.8272 (tp30) cc_final: 0.7655 (tp30) REVERT: M 128 ASN cc_start: 0.8367 (m-40) cc_final: 0.7933 (m-40) REVERT: M 131 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8156 (mttp) REVERT: M 134 ILE cc_start: 0.8382 (mt) cc_final: 0.8137 (tp) REVERT: M 135 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8405 (mmtt) REVERT: M 161 GLN cc_start: 0.8372 (tp40) cc_final: 0.8082 (tp-100) REVERT: M 201 GLU cc_start: 0.5751 (tm-30) cc_final: 0.4982 (tm-30) REVERT: M 203 GLN cc_start: 0.7228 (mm110) cc_final: 0.6814 (mm-40) REVERT: M 209 CYS cc_start: 0.7389 (t) cc_final: 0.6379 (m) REVERT: M 220 LEU cc_start: 0.8224 (mm) cc_final: 0.7808 (mm) REVERT: M 234 HIS cc_start: 0.8060 (t-90) cc_final: 0.7753 (t-90) REVERT: M 242 TRP cc_start: 0.7763 (t-100) cc_final: 0.7232 (t-100) REVERT: M 245 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6245 (mm-30) REVERT: M 257 PHE cc_start: 0.8209 (p90) cc_final: 0.7830 (p90) REVERT: M 258 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7758 (mtm180) REVERT: M 262 TYR cc_start: 0.8360 (p90) cc_final: 0.8109 (p90) REVERT: M 298 LYS cc_start: 0.9038 (tttt) cc_final: 0.8659 (tttt) REVERT: M 377 PHE cc_start: 0.7784 (p90) cc_final: 0.7569 (p90) REVERT: M 384 ILE cc_start: 0.8558 (tt) cc_final: 0.8341 (tt) REVERT: M 393 ASP cc_start: 0.7771 (t0) cc_final: 0.7437 (t0) REVERT: M 400 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8664 (mmtt) REVERT: M 406 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8311 (ttmt) REVERT: M 414 PHE cc_start: 0.7801 (t80) cc_final: 0.7149 (t80) REVERT: C 23 VAL cc_start: 0.8784 (m) cc_final: 0.8403 (m) REVERT: C 44 THR cc_start: 0.9126 (m) cc_final: 0.8710 (p) REVERT: C 68 VAL cc_start: 0.8173 (t) cc_final: 0.7892 (p) REVERT: C 78 TRP cc_start: 0.8320 (m-10) cc_final: 0.7977 (m-10) REVERT: C 79 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8376 (mtm110) REVERT: C 81 TYR cc_start: 0.7192 (m-80) cc_final: 0.6443 (m-80) REVERT: C 82 PHE cc_start: 0.8180 (m-80) cc_final: 0.7810 (m-80) REVERT: C 84 ASN cc_start: 0.8548 (t0) cc_final: 0.7893 (t0) REVERT: C 95 ASN cc_start: 0.7756 (t0) cc_final: 0.7420 (t0) REVERT: C 142 LYS cc_start: 0.8994 (mttm) cc_final: 0.8745 (mttm) REVERT: C 168 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 171 ASP cc_start: 0.8130 (m-30) cc_final: 0.7791 (m-30) REVERT: b 43 LYS cc_start: 0.8147 (mttt) cc_final: 0.7703 (tptm) REVERT: b 47 LEU cc_start: 0.8983 (mt) cc_final: 0.8513 (mt) REVERT: b 48 LYS cc_start: 0.8994 (ptpp) cc_final: 0.8130 (ptpp) REVERT: b 50 MET cc_start: 0.8545 (mtm) cc_final: 0.8130 (mtm) REVERT: b 51 LEU cc_start: 0.8765 (mt) cc_final: 0.8355 (mt) REVERT: b 52 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7865 (mm-30) REVERT: b 54 ASN cc_start: 0.7984 (m110) cc_final: 0.7764 (m110) REVERT: b 63 MET cc_start: 0.8795 (mmm) cc_final: 0.8133 (mmm) REVERT: b 80 PHE cc_start: 0.8451 (t80) cc_final: 0.7808 (t80) REVERT: b 99 TYR cc_start: 0.8533 (m-80) cc_final: 0.8164 (m-80) REVERT: b 107 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7451 (mt-10) REVERT: b 112 LEU cc_start: 0.8206 (mp) cc_final: 0.7195 (mp) REVERT: b 121 GLN cc_start: 0.8153 (tt0) cc_final: 0.7874 (mt0) REVERT: b 124 LEU cc_start: 0.8950 (tp) cc_final: 0.8695 (tt) REVERT: b 128 ASN cc_start: 0.8183 (t0) cc_final: 0.7727 (t0) REVERT: b 132 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8121 (mtm180) REVERT: b 147 ILE cc_start: 0.8365 (pt) cc_final: 0.7677 (pt) REVERT: b 150 ILE cc_start: 0.8281 (mt) cc_final: 0.7997 (mt) REVERT: b 151 MET cc_start: 0.7586 (mtp) cc_final: 0.6926 (mtp) REVERT: b 152 MET cc_start: 0.8039 (tpt) cc_final: 0.7832 (tpt) REVERT: b 162 LEU cc_start: 0.8004 (mp) cc_final: 0.7148 (tp) REVERT: b 190 GLU cc_start: 0.8082 (tt0) cc_final: 0.7794 (tt0) REVERT: b 195 LEU cc_start: 0.9035 (mt) cc_final: 0.8768 (tt) REVERT: b 199 LYS cc_start: 0.8079 (mppt) cc_final: 0.7823 (mmtm) REVERT: b 202 LEU cc_start: 0.7735 (mm) cc_final: 0.7252 (tp) REVERT: b 212 GLU cc_start: 0.8189 (tp30) cc_final: 0.7773 (tp30) REVERT: b 215 CYS cc_start: 0.8879 (m) cc_final: 0.8340 (p) REVERT: b 228 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8242 (ttpt) REVERT: b 237 GLU cc_start: 0.7581 (tt0) cc_final: 0.7084 (tt0) REVERT: b 241 GLN cc_start: 0.8067 (mt0) cc_final: 0.7486 (mt0) REVERT: b 244 ILE cc_start: 0.9100 (mt) cc_final: 0.8654 (tp) REVERT: b 247 MET cc_start: 0.7492 (tmm) cc_final: 0.6861 (tmm) REVERT: b 307 LEU cc_start: 0.8855 (mt) cc_final: 0.8432 (mt) REVERT: b 308 LEU cc_start: 0.8804 (mt) cc_final: 0.8492 (mm) REVERT: b 311 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7705 (ptt-90) REVERT: b 317 MET cc_start: 0.8618 (tpp) cc_final: 0.8275 (tpp) REVERT: b 322 LEU cc_start: 0.8483 (tt) cc_final: 0.8257 (tt) REVERT: b 326 ILE cc_start: 0.8013 (mm) cc_final: 0.7721 (mm) REVERT: b 331 GLU cc_start: 0.7153 (mp0) cc_final: 0.6702 (mp0) REVERT: b 341 ARG cc_start: 0.8634 (ptt90) cc_final: 0.8253 (ptm-80) REVERT: b 346 ASN cc_start: 0.7301 (p0) cc_final: 0.6812 (p0) REVERT: b 352 ILE cc_start: 0.8660 (mm) cc_final: 0.8442 (mm) REVERT: b 363 GLN cc_start: 0.8859 (mp10) cc_final: 0.8527 (mp10) REVERT: b 384 MET cc_start: 0.7926 (ptt) cc_final: 0.7445 (ptt) REVERT: b 391 GLU cc_start: 0.8233 (tp30) cc_final: 0.8018 (tp30) REVERT: b 629 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7778 (ttmm) REVERT: m 1 MET cc_start: 0.6976 (mtt) cc_final: 0.6663 (mtt) REVERT: m 17 GLU cc_start: 0.7596 (pt0) cc_final: 0.7270 (pt0) REVERT: m 29 CYS cc_start: 0.8527 (m) cc_final: 0.7902 (t) REVERT: m 36 GLN cc_start: 0.8369 (tp-100) cc_final: 0.7993 (tp-100) REVERT: m 43 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7471 (mt-10) REVERT: m 44 ASN cc_start: 0.8359 (t0) cc_final: 0.7552 (t0) REVERT: m 45 VAL cc_start: 0.8884 (t) cc_final: 0.8664 (t) REVERT: m 71 GLN cc_start: 0.8311 (tp40) cc_final: 0.8025 (tp-100) REVERT: m 72 THR cc_start: 0.8536 (p) cc_final: 0.8319 (p) REVERT: m 80 ILE cc_start: 0.8574 (mt) cc_final: 0.8302 (mm) REVERT: m 88 ASP cc_start: 0.8418 (m-30) cc_final: 0.8108 (m-30) REVERT: m 89 THR cc_start: 0.8965 (m) cc_final: 0.8629 (p) REVERT: m 108 ILE cc_start: 0.8907 (mt) cc_final: 0.8551 (mm) REVERT: m 111 GLU cc_start: 0.8061 (tt0) cc_final: 0.7801 (tt0) REVERT: m 116 MET cc_start: 0.7699 (mtm) cc_final: 0.7369 (mtm) REVERT: m 123 LEU cc_start: 0.8347 (tp) cc_final: 0.8078 (tp) REVERT: m 126 GLU cc_start: 0.8316 (tp30) cc_final: 0.7512 (tp30) REVERT: m 128 ASN cc_start: 0.8242 (m-40) cc_final: 0.7627 (m-40) REVERT: m 129 ILE cc_start: 0.8915 (mm) cc_final: 0.8603 (tp) REVERT: m 131 LYS cc_start: 0.8548 (mttp) cc_final: 0.8141 (mttp) REVERT: m 134 ILE cc_start: 0.8235 (mt) cc_final: 0.7697 (tp) REVERT: m 140 LEU cc_start: 0.8489 (mt) cc_final: 0.8238 (tt) REVERT: m 141 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7729 (mmt90) REVERT: m 157 LEU cc_start: 0.8464 (mt) cc_final: 0.8234 (pp) REVERT: m 161 GLN cc_start: 0.8301 (tp40) cc_final: 0.7959 (tp-100) REVERT: m 209 CYS cc_start: 0.7384 (t) cc_final: 0.6464 (m) REVERT: m 220 LEU cc_start: 0.8186 (mm) cc_final: 0.7870 (mm) REVERT: m 234 HIS cc_start: 0.8070 (t-90) cc_final: 0.7662 (t-90) REVERT: m 240 LYS cc_start: 0.8556 (mttt) cc_final: 0.7817 (mmmm) REVERT: m 243 GLU cc_start: 0.8616 (tp30) cc_final: 0.8263 (tp30) REVERT: m 257 PHE cc_start: 0.8505 (p90) cc_final: 0.8182 (p90) REVERT: m 258 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8075 (mtm180) REVERT: m 262 TYR cc_start: 0.8186 (p90) cc_final: 0.6930 (p90) REVERT: m 298 LYS cc_start: 0.9067 (tttt) cc_final: 0.8702 (tttt) REVERT: m 378 LYS cc_start: 0.8071 (pttt) cc_final: 0.7777 (pttt) REVERT: m 387 LEU cc_start: 0.8692 (tp) cc_final: 0.7853 (pt) REVERT: m 393 ASP cc_start: 0.8105 (t0) cc_final: 0.7631 (t0) REVERT: m 402 PHE cc_start: 0.7770 (m-80) cc_final: 0.7218 (m-10) REVERT: m 407 TYR cc_start: 0.8622 (m-80) cc_final: 0.8075 (m-80) REVERT: m 414 PHE cc_start: 0.7855 (t80) cc_final: 0.7543 (t80) REVERT: c 44 THR cc_start: 0.9199 (m) cc_final: 0.8774 (p) REVERT: c 45 THR cc_start: 0.8758 (p) cc_final: 0.8521 (p) REVERT: c 53 VAL cc_start: 0.8692 (t) cc_final: 0.8420 (m) REVERT: c 64 THR cc_start: 0.6544 (m) cc_final: 0.6226 (t) REVERT: c 78 TRP cc_start: 0.8343 (m-10) cc_final: 0.7411 (m-10) REVERT: c 84 ASN cc_start: 0.8474 (t0) cc_final: 0.7676 (t0) REVERT: c 97 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7699 (mmm-85) REVERT: c 110 MET cc_start: 0.8494 (mmm) cc_final: 0.7907 (mmm) REVERT: c 115 GLU cc_start: 0.7856 (tt0) cc_final: 0.7491 (tt0) REVERT: c 171 ASP cc_start: 0.8136 (m-30) cc_final: 0.7699 (m-30) REVERT: c 178 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7648 (ttm170) REVERT: y 415 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7508 (mm110) outliers start: 1 outliers final: 0 residues processed: 767 average time/residue: 0.3228 time to fit residues: 351.0851 Evaluate side-chains 750 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 750 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN M 54 HIS Y 411 HIS b 231 ASN m 26 GLN m 54 HIS c 95 ASN c 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110654 restraints weight = 30762.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114905 restraints weight = 16730.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117841 restraints weight = 10450.263| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16108 Z= 0.235 Angle : 0.607 8.718 21822 Z= 0.321 Chirality : 0.046 0.166 2524 Planarity : 0.005 0.047 2752 Dihedral : 9.575 162.956 2154 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.11 (0.20), residues: 1954 helix: 1.14 (0.18), residues: 818 sheet: 0.32 (0.28), residues: 378 loop : 0.74 (0.25), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP C 172 HIS 0.004 0.001 HIS b 624 PHE 0.018 0.002 PHE C 51 TYR 0.025 0.002 TYR c 58 ARG 0.009 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 1.823 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 43 LYS cc_start: 0.8147 (mttt) cc_final: 0.7601 (tptt) REVERT: B 45 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 47 LEU cc_start: 0.9040 (mt) cc_final: 0.8674 (mt) REVERT: B 48 LYS cc_start: 0.9145 (mtmt) cc_final: 0.8547 (mttt) REVERT: B 50 MET cc_start: 0.8679 (mtm) cc_final: 0.8259 (mtm) REVERT: B 51 LEU cc_start: 0.8793 (mt) cc_final: 0.8499 (mt) REVERT: B 52 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 54 ASN cc_start: 0.8112 (m110) cc_final: 0.7822 (m110) REVERT: B 55 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7699 (mtpp) REVERT: B 59 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8637 (mttt) REVERT: B 63 MET cc_start: 0.8677 (mmm) cc_final: 0.8254 (mmm) REVERT: B 72 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8598 (ttmt) REVERT: B 74 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8109 (mmtt) REVERT: B 80 PHE cc_start: 0.8603 (t80) cc_final: 0.8019 (t80) REVERT: B 85 LYS cc_start: 0.8568 (mttt) cc_final: 0.7758 (mttt) REVERT: B 90 LYS cc_start: 0.8565 (mttt) cc_final: 0.7811 (mmmm) REVERT: B 101 TYR cc_start: 0.8739 (t80) cc_final: 0.8431 (t80) REVERT: B 107 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7447 (mt-10) REVERT: B 112 LEU cc_start: 0.8377 (mp) cc_final: 0.7518 (mp) REVERT: B 121 GLN cc_start: 0.8428 (tt0) cc_final: 0.8083 (tt0) REVERT: B 125 LYS cc_start: 0.8975 (mttt) cc_final: 0.8484 (mtpp) REVERT: B 132 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8372 (mtm-85) REVERT: B 137 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7376 (mtp-110) REVERT: B 141 SER cc_start: 0.8686 (m) cc_final: 0.8212 (p) REVERT: B 147 ILE cc_start: 0.8436 (pt) cc_final: 0.7535 (pt) REVERT: B 150 ILE cc_start: 0.8515 (mp) cc_final: 0.8268 (tp) REVERT: B 151 MET cc_start: 0.7785 (mtp) cc_final: 0.7097 (mtp) REVERT: B 152 MET cc_start: 0.7947 (tpt) cc_final: 0.7746 (tpt) REVERT: B 155 ILE cc_start: 0.9225 (mm) cc_final: 0.8919 (mm) REVERT: B 175 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 183 GLU cc_start: 0.8485 (mp0) cc_final: 0.8076 (mp0) REVERT: B 190 GLU cc_start: 0.8117 (tt0) cc_final: 0.7851 (tt0) REVERT: B 193 GLU cc_start: 0.8457 (tt0) cc_final: 0.8088 (tt0) REVERT: B 199 LYS cc_start: 0.8070 (mppt) cc_final: 0.7816 (mmtm) REVERT: B 202 LEU cc_start: 0.7763 (mm) cc_final: 0.7282 (tp) REVERT: B 213 GLU cc_start: 0.7971 (tt0) cc_final: 0.7701 (tt0) REVERT: B 215 CYS cc_start: 0.8931 (m) cc_final: 0.8438 (p) REVERT: B 221 LEU cc_start: 0.9161 (mt) cc_final: 0.8794 (pp) REVERT: B 228 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8147 (ttpt) REVERT: B 246 HIS cc_start: 0.8382 (m-70) cc_final: 0.8111 (m-70) REVERT: B 247 MET cc_start: 0.7214 (tmm) cc_final: 0.6830 (tmm) REVERT: B 308 LEU cc_start: 0.8655 (mt) cc_final: 0.8263 (mm) REVERT: B 311 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7540 (ptt90) REVERT: B 317 MET cc_start: 0.8573 (tpp) cc_final: 0.8218 (tpp) REVERT: B 321 GLN cc_start: 0.8119 (tt0) cc_final: 0.7362 (tt0) REVERT: B 322 LEU cc_start: 0.8402 (tt) cc_final: 0.8170 (tt) REVERT: B 324 TRP cc_start: 0.8763 (t-100) cc_final: 0.8468 (t-100) REVERT: B 326 ILE cc_start: 0.7973 (mm) cc_final: 0.7677 (mm) REVERT: B 341 ARG cc_start: 0.8731 (ptt90) cc_final: 0.8258 (ptm-80) REVERT: B 346 ASN cc_start: 0.7270 (p0) cc_final: 0.6676 (p0) REVERT: B 360 MET cc_start: 0.8527 (tpp) cc_final: 0.7498 (tpp) REVERT: B 389 LYS cc_start: 0.8981 (mttt) cc_final: 0.8214 (mmmm) REVERT: B 391 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 417 ASP cc_start: 0.8475 (m-30) cc_final: 0.8176 (m-30) REVERT: M 17 GLU cc_start: 0.7546 (pt0) cc_final: 0.7268 (pt0) REVERT: M 26 GLN cc_start: 0.8360 (mt0) cc_final: 0.7881 (tp-100) REVERT: M 29 CYS cc_start: 0.8745 (t) cc_final: 0.8286 (t) REVERT: M 31 TYR cc_start: 0.8231 (m-80) cc_final: 0.7801 (m-10) REVERT: M 34 GLU cc_start: 0.8983 (tt0) cc_final: 0.8658 (tt0) REVERT: M 41 ASP cc_start: 0.8537 (t0) cc_final: 0.8253 (t0) REVERT: M 43 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7486 (mt-10) REVERT: M 63 LYS cc_start: 0.8285 (mttt) cc_final: 0.7465 (tmtt) REVERT: M 71 GLN cc_start: 0.8385 (mm110) cc_final: 0.7930 (mm110) REVERT: M 78 PHE cc_start: 0.8734 (t80) cc_final: 0.8515 (t80) REVERT: M 88 ASP cc_start: 0.8421 (m-30) cc_final: 0.8158 (m-30) REVERT: M 89 THR cc_start: 0.9185 (m) cc_final: 0.8927 (p) REVERT: M 116 MET cc_start: 0.8034 (mtm) cc_final: 0.7611 (mtm) REVERT: M 126 GLU cc_start: 0.8330 (tp30) cc_final: 0.7624 (tp30) REVERT: M 128 ASN cc_start: 0.8384 (m-40) cc_final: 0.7959 (m-40) REVERT: M 131 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8277 (mttp) REVERT: M 134 ILE cc_start: 0.8365 (mt) cc_final: 0.8132 (tp) REVERT: M 135 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8406 (mmtt) REVERT: M 152 ASN cc_start: 0.7893 (m-40) cc_final: 0.7628 (m-40) REVERT: M 161 GLN cc_start: 0.8381 (tp40) cc_final: 0.8121 (tp-100) REVERT: M 172 VAL cc_start: 0.8790 (t) cc_final: 0.8456 (t) REVERT: M 201 GLU cc_start: 0.5658 (tm-30) cc_final: 0.4785 (tm-30) REVERT: M 203 GLN cc_start: 0.7212 (mm110) cc_final: 0.6805 (mm-40) REVERT: M 209 CYS cc_start: 0.7396 (t) cc_final: 0.6556 (m) REVERT: M 220 LEU cc_start: 0.8277 (mm) cc_final: 0.7883 (mm) REVERT: M 234 HIS cc_start: 0.8148 (t-90) cc_final: 0.7732 (t-90) REVERT: M 242 TRP cc_start: 0.7888 (t-100) cc_final: 0.7288 (t-100) REVERT: M 245 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6332 (mm-30) REVERT: M 257 PHE cc_start: 0.8207 (p90) cc_final: 0.7948 (p90) REVERT: M 258 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7859 (mtm180) REVERT: M 262 TYR cc_start: 0.8359 (p90) cc_final: 0.8093 (p90) REVERT: M 298 LYS cc_start: 0.9063 (tttt) cc_final: 0.8684 (tttt) REVERT: M 384 ILE cc_start: 0.8605 (tt) cc_final: 0.8393 (tt) REVERT: M 393 ASP cc_start: 0.7690 (t0) cc_final: 0.7361 (t0) REVERT: M 400 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8711 (mmtt) REVERT: M 406 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8351 (ttmt) REVERT: M 414 PHE cc_start: 0.7806 (t80) cc_final: 0.7197 (t80) REVERT: C 23 VAL cc_start: 0.8805 (m) cc_final: 0.8489 (m) REVERT: C 44 THR cc_start: 0.9119 (m) cc_final: 0.8654 (p) REVERT: C 68 VAL cc_start: 0.8222 (t) cc_final: 0.7957 (p) REVERT: C 78 TRP cc_start: 0.8329 (m-10) cc_final: 0.7963 (m-10) REVERT: C 81 TYR cc_start: 0.7184 (m-80) cc_final: 0.6432 (m-80) REVERT: C 82 PHE cc_start: 0.8218 (m-80) cc_final: 0.7447 (m-80) REVERT: C 84 ASN cc_start: 0.8507 (t0) cc_final: 0.7766 (t0) REVERT: C 95 ASN cc_start: 0.7815 (t0) cc_final: 0.7485 (t0) REVERT: C 115 GLU cc_start: 0.8054 (tt0) cc_final: 0.7852 (tt0) REVERT: C 168 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 171 ASP cc_start: 0.7997 (m-30) cc_final: 0.7704 (m-30) REVERT: b 43 LYS cc_start: 0.8138 (mttt) cc_final: 0.7616 (tptm) REVERT: b 47 LEU cc_start: 0.9019 (mt) cc_final: 0.8615 (mt) REVERT: b 48 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8209 (ptpp) REVERT: b 50 MET cc_start: 0.8506 (mtm) cc_final: 0.8240 (mtm) REVERT: b 52 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7867 (mm-30) REVERT: b 54 ASN cc_start: 0.8068 (m110) cc_final: 0.7834 (m-40) REVERT: b 63 MET cc_start: 0.8760 (mmm) cc_final: 0.8055 (mmm) REVERT: b 72 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8483 (mmtt) REVERT: b 80 PHE cc_start: 0.8465 (t80) cc_final: 0.7982 (t80) REVERT: b 101 TYR cc_start: 0.8820 (t80) cc_final: 0.8610 (t80) REVERT: b 102 LEU cc_start: 0.8942 (mt) cc_final: 0.8720 (mt) REVERT: b 107 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7499 (mt-10) REVERT: b 112 LEU cc_start: 0.8247 (mp) cc_final: 0.7557 (mp) REVERT: b 119 THR cc_start: 0.8411 (t) cc_final: 0.8182 (m) REVERT: b 124 LEU cc_start: 0.8938 (tp) cc_final: 0.8682 (tt) REVERT: b 128 ASN cc_start: 0.8282 (t0) cc_final: 0.7848 (t0) REVERT: b 132 ARG cc_start: 0.8396 (mtt180) cc_final: 0.8137 (mtm180) REVERT: b 137 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7432 (mtp85) REVERT: b 147 ILE cc_start: 0.8394 (pt) cc_final: 0.7627 (pt) REVERT: b 151 MET cc_start: 0.7606 (mtp) cc_final: 0.6941 (mtp) REVERT: b 152 MET cc_start: 0.8027 (tpt) cc_final: 0.7810 (tpt) REVERT: b 162 LEU cc_start: 0.7936 (mp) cc_final: 0.7134 (tp) REVERT: b 190 GLU cc_start: 0.8010 (tt0) cc_final: 0.7732 (tt0) REVERT: b 195 LEU cc_start: 0.9045 (mt) cc_final: 0.8747 (tt) REVERT: b 199 LYS cc_start: 0.8095 (mppt) cc_final: 0.7842 (mmtm) REVERT: b 202 LEU cc_start: 0.7810 (mm) cc_final: 0.7321 (tt) REVERT: b 212 GLU cc_start: 0.8158 (tp30) cc_final: 0.7737 (tp30) REVERT: b 215 CYS cc_start: 0.8912 (m) cc_final: 0.8394 (p) REVERT: b 225 ASN cc_start: 0.8113 (m-40) cc_final: 0.7227 (m-40) REVERT: b 228 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8323 (ttpt) REVERT: b 237 GLU cc_start: 0.7642 (tt0) cc_final: 0.7126 (tt0) REVERT: b 241 GLN cc_start: 0.8129 (mt0) cc_final: 0.7497 (mt0) REVERT: b 244 ILE cc_start: 0.9124 (mt) cc_final: 0.8693 (tp) REVERT: b 302 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8585 (ttm-80) REVERT: b 307 LEU cc_start: 0.8841 (mt) cc_final: 0.8452 (mt) REVERT: b 308 LEU cc_start: 0.8817 (mt) cc_final: 0.8505 (mm) REVERT: b 311 ARG cc_start: 0.8267 (ptt180) cc_final: 0.7713 (ptt-90) REVERT: b 317 MET cc_start: 0.8616 (tpp) cc_final: 0.8257 (tpp) REVERT: b 321 GLN cc_start: 0.8057 (tt0) cc_final: 0.7432 (tt0) REVERT: b 324 TRP cc_start: 0.8610 (t-100) cc_final: 0.8125 (t-100) REVERT: b 326 ILE cc_start: 0.8016 (mm) cc_final: 0.7763 (mm) REVERT: b 341 ARG cc_start: 0.8675 (ptt90) cc_final: 0.8296 (ptm-80) REVERT: b 346 ASN cc_start: 0.7478 (p0) cc_final: 0.6925 (p0) REVERT: b 355 GLN cc_start: 0.8692 (mt0) cc_final: 0.8425 (mt0) REVERT: b 360 MET cc_start: 0.8242 (tpp) cc_final: 0.7069 (tpp) REVERT: b 363 GLN cc_start: 0.8883 (mp10) cc_final: 0.8667 (mp10) REVERT: b 384 MET cc_start: 0.7928 (ptt) cc_final: 0.7390 (ptt) REVERT: b 391 GLU cc_start: 0.8252 (tp30) cc_final: 0.8051 (tp30) REVERT: b 629 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8124 (ttmt) REVERT: b 640 PRO cc_start: 0.8624 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: m 17 GLU cc_start: 0.7612 (pt0) cc_final: 0.7304 (pt0) REVERT: m 21 LYS cc_start: 0.8054 (mttt) cc_final: 0.7514 (mttm) REVERT: m 29 CYS cc_start: 0.8536 (m) cc_final: 0.7897 (t) REVERT: m 36 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7967 (tp-100) REVERT: m 43 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7429 (mt-10) REVERT: m 44 ASN cc_start: 0.8380 (t0) cc_final: 0.7541 (t0) REVERT: m 45 VAL cc_start: 0.8909 (t) cc_final: 0.8662 (t) REVERT: m 71 GLN cc_start: 0.8355 (tp40) cc_final: 0.8037 (tp40) REVERT: m 74 VAL cc_start: 0.8985 (t) cc_final: 0.8550 (t) REVERT: m 77 LEU cc_start: 0.8620 (mt) cc_final: 0.8368 (mt) REVERT: m 80 ILE cc_start: 0.8612 (mt) cc_final: 0.8357 (mm) REVERT: m 82 PHE cc_start: 0.8243 (t80) cc_final: 0.8036 (t80) REVERT: m 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8082 (m-30) REVERT: m 108 ILE cc_start: 0.8954 (mt) cc_final: 0.8597 (mm) REVERT: m 111 GLU cc_start: 0.8038 (tt0) cc_final: 0.7833 (tt0) REVERT: m 116 MET cc_start: 0.7719 (mtm) cc_final: 0.7416 (mtm) REVERT: m 126 GLU cc_start: 0.8303 (tp30) cc_final: 0.7572 (tp30) REVERT: m 128 ASN cc_start: 0.8203 (m-40) cc_final: 0.7545 (m-40) REVERT: m 129 ILE cc_start: 0.8918 (mm) cc_final: 0.8622 (tp) REVERT: m 131 LYS cc_start: 0.8650 (mttp) cc_final: 0.7995 (mtmm) REVERT: m 134 ILE cc_start: 0.8317 (mt) cc_final: 0.8014 (tp) REVERT: m 140 LEU cc_start: 0.8510 (mt) cc_final: 0.8249 (tt) REVERT: m 141 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7694 (mmt90) REVERT: m 161 GLN cc_start: 0.8313 (tp40) cc_final: 0.7963 (tp-100) REVERT: m 203 GLN cc_start: 0.7128 (mm110) cc_final: 0.6862 (mm-40) REVERT: m 209 CYS cc_start: 0.7463 (t) cc_final: 0.6440 (m) REVERT: m 220 LEU cc_start: 0.8238 (mm) cc_final: 0.7966 (mm) REVERT: m 234 HIS cc_start: 0.8034 (t-90) cc_final: 0.7620 (t-90) REVERT: m 240 LYS cc_start: 0.8572 (mttt) cc_final: 0.7795 (mmmm) REVERT: m 243 GLU cc_start: 0.8600 (tp30) cc_final: 0.8250 (tp30) REVERT: m 257 PHE cc_start: 0.8527 (p90) cc_final: 0.8201 (p90) REVERT: m 258 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8105 (mtm180) REVERT: m 262 TYR cc_start: 0.8191 (p90) cc_final: 0.7004 (p90) REVERT: m 272 ILE cc_start: 0.8149 (mm) cc_final: 0.7694 (tp) REVERT: m 378 LYS cc_start: 0.8017 (pttt) cc_final: 0.7776 (pttt) REVERT: m 387 LEU cc_start: 0.8698 (tp) cc_final: 0.7935 (pt) REVERT: m 393 ASP cc_start: 0.8100 (t0) cc_final: 0.7625 (t0) REVERT: m 402 PHE cc_start: 0.7782 (m-80) cc_final: 0.7406 (m-10) REVERT: m 407 TYR cc_start: 0.8670 (m-80) cc_final: 0.8104 (m-80) REVERT: m 414 PHE cc_start: 0.7851 (t80) cc_final: 0.7581 (t80) REVERT: c 53 VAL cc_start: 0.8693 (t) cc_final: 0.8418 (m) REVERT: c 64 THR cc_start: 0.6561 (m) cc_final: 0.6244 (t) REVERT: c 78 TRP cc_start: 0.8369 (m-10) cc_final: 0.7526 (m-10) REVERT: c 82 PHE cc_start: 0.8050 (m-10) cc_final: 0.7749 (m-80) REVERT: c 84 ASN cc_start: 0.8468 (t0) cc_final: 0.7513 (t0) REVERT: c 97 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7749 (mmm-85) REVERT: c 110 MET cc_start: 0.8486 (mmm) cc_final: 0.7817 (mmm) REVERT: c 115 GLU cc_start: 0.7856 (tt0) cc_final: 0.7520 (tt0) REVERT: c 168 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7672 (mt-10) REVERT: c 171 ASP cc_start: 0.8192 (m-30) cc_final: 0.7712 (m-30) REVERT: y 415 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7516 (mm110) outliers start: 0 outliers final: 0 residues processed: 760 average time/residue: 0.3161 time to fit residues: 340.3643 Evaluate side-chains 744 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 189 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 54 HIS C 176 GLN Y 411 HIS b 231 ASN b 303 ASN m 26 GLN c 86 GLN c 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112666 restraints weight = 30794.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117005 restraints weight = 16619.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120054 restraints weight = 10316.623| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16108 Z= 0.181 Angle : 0.597 8.267 21822 Z= 0.310 Chirality : 0.045 0.189 2524 Planarity : 0.004 0.047 2752 Dihedral : 9.309 160.584 2154 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.14 (0.20), residues: 1954 helix: 1.23 (0.19), residues: 816 sheet: 0.27 (0.27), residues: 388 loop : 0.73 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP c 172 HIS 0.005 0.001 HIS b 246 PHE 0.025 0.002 PHE m 121 TYR 0.026 0.002 TYR B 351 ARG 0.010 0.000 ARG C 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 1.797 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: B 43 LYS cc_start: 0.8188 (mttt) cc_final: 0.7621 (tptt) REVERT: B 44 ASN cc_start: 0.8681 (m110) cc_final: 0.8360 (m-40) REVERT: B 45 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7157 (mm-30) REVERT: B 47 LEU cc_start: 0.9059 (mt) cc_final: 0.8628 (mt) REVERT: B 48 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8510 (mttt) REVERT: B 50 MET cc_start: 0.8633 (mtm) cc_final: 0.8190 (mtm) REVERT: B 51 LEU cc_start: 0.8784 (mt) cc_final: 0.8483 (mt) REVERT: B 52 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 54 ASN cc_start: 0.8127 (m110) cc_final: 0.7775 (m110) REVERT: B 55 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7667 (mtpp) REVERT: B 59 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8598 (mttt) REVERT: B 63 MET cc_start: 0.8703 (mmm) cc_final: 0.8307 (mmm) REVERT: B 69 MET cc_start: 0.8198 (mtm) cc_final: 0.7990 (mtm) REVERT: B 72 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8569 (ttmt) REVERT: B 74 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8121 (mmtt) REVERT: B 80 PHE cc_start: 0.8611 (t80) cc_final: 0.8014 (t80) REVERT: B 83 VAL cc_start: 0.8305 (t) cc_final: 0.8095 (t) REVERT: B 85 LYS cc_start: 0.8581 (mttt) cc_final: 0.7736 (mttt) REVERT: B 90 LYS cc_start: 0.8523 (mttt) cc_final: 0.7780 (mmmm) REVERT: B 101 TYR cc_start: 0.8732 (t80) cc_final: 0.8366 (t80) REVERT: B 107 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 112 LEU cc_start: 0.8378 (mp) cc_final: 0.7494 (mp) REVERT: B 121 GLN cc_start: 0.8381 (tt0) cc_final: 0.8179 (mt0) REVERT: B 125 LYS cc_start: 0.8963 (mttt) cc_final: 0.8466 (mtpp) REVERT: B 130 LEU cc_start: 0.8686 (tp) cc_final: 0.8434 (tp) REVERT: B 137 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7377 (mtp-110) REVERT: B 141 SER cc_start: 0.8650 (m) cc_final: 0.6877 (p) REVERT: B 142 ILE cc_start: 0.9156 (mm) cc_final: 0.8936 (mm) REVERT: B 143 ARG cc_start: 0.7457 (mpt180) cc_final: 0.7110 (mpt180) REVERT: B 147 ILE cc_start: 0.8318 (pt) cc_final: 0.7582 (pt) REVERT: B 151 MET cc_start: 0.7775 (mtp) cc_final: 0.6985 (mtp) REVERT: B 152 MET cc_start: 0.7974 (tpt) cc_final: 0.7715 (tpt) REVERT: B 155 ILE cc_start: 0.9194 (mm) cc_final: 0.8961 (mm) REVERT: B 175 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 181 ASP cc_start: 0.8528 (t0) cc_final: 0.8007 (t0) REVERT: B 183 GLU cc_start: 0.8487 (mp0) cc_final: 0.8266 (mp0) REVERT: B 185 LYS cc_start: 0.8537 (tttp) cc_final: 0.8159 (tptp) REVERT: B 190 GLU cc_start: 0.8130 (tt0) cc_final: 0.7763 (tt0) REVERT: B 193 GLU cc_start: 0.8466 (tt0) cc_final: 0.8095 (tt0) REVERT: B 199 LYS cc_start: 0.7976 (mppt) cc_final: 0.7748 (mmtm) REVERT: B 202 LEU cc_start: 0.7425 (mm) cc_final: 0.7014 (tp) REVERT: B 213 GLU cc_start: 0.7981 (tt0) cc_final: 0.7707 (tt0) REVERT: B 221 LEU cc_start: 0.9189 (mt) cc_final: 0.8831 (pp) REVERT: B 228 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8150 (ttpt) REVERT: B 237 GLU cc_start: 0.7812 (tt0) cc_final: 0.7491 (tt0) REVERT: B 241 GLN cc_start: 0.8216 (mt0) cc_final: 0.7834 (mt0) REVERT: B 247 MET cc_start: 0.7186 (tmm) cc_final: 0.6890 (tmm) REVERT: B 308 LEU cc_start: 0.8651 (mt) cc_final: 0.8304 (mm) REVERT: B 311 ARG cc_start: 0.8009 (ptt180) cc_final: 0.7517 (ptt90) REVERT: B 317 MET cc_start: 0.8563 (tpp) cc_final: 0.8240 (tpp) REVERT: B 321 GLN cc_start: 0.8110 (tt0) cc_final: 0.7404 (tt0) REVERT: B 322 LEU cc_start: 0.8346 (tt) cc_final: 0.8113 (tt) REVERT: B 324 TRP cc_start: 0.8751 (t-100) cc_final: 0.8445 (t-100) REVERT: B 326 ILE cc_start: 0.7934 (mm) cc_final: 0.7639 (mm) REVERT: B 341 ARG cc_start: 0.8726 (ptt90) cc_final: 0.8253 (ptm-80) REVERT: B 346 ASN cc_start: 0.7176 (p0) cc_final: 0.6222 (p0) REVERT: B 348 GLU cc_start: 0.8129 (mp0) cc_final: 0.7781 (mp0) REVERT: B 360 MET cc_start: 0.8420 (tpp) cc_final: 0.7199 (tpp) REVERT: B 389 LYS cc_start: 0.8980 (mttt) cc_final: 0.8308 (ttmm) REVERT: B 391 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 417 ASP cc_start: 0.8476 (m-30) cc_final: 0.8189 (m-30) REVERT: M 17 GLU cc_start: 0.7487 (pt0) cc_final: 0.7140 (pt0) REVERT: M 29 CYS cc_start: 0.8713 (t) cc_final: 0.8253 (t) REVERT: M 31 TYR cc_start: 0.8231 (m-80) cc_final: 0.7803 (m-10) REVERT: M 34 GLU cc_start: 0.8999 (tt0) cc_final: 0.8623 (tt0) REVERT: M 41 ASP cc_start: 0.8482 (t0) cc_final: 0.8245 (t0) REVERT: M 43 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7422 (mt-10) REVERT: M 70 ILE cc_start: 0.8347 (mm) cc_final: 0.8143 (mm) REVERT: M 71 GLN cc_start: 0.8404 (mm110) cc_final: 0.8061 (mm-40) REVERT: M 88 ASP cc_start: 0.8372 (m-30) cc_final: 0.8134 (m-30) REVERT: M 89 THR cc_start: 0.9164 (m) cc_final: 0.8897 (p) REVERT: M 103 LYS cc_start: 0.7223 (mtmm) cc_final: 0.6984 (mtmm) REVERT: M 116 MET cc_start: 0.8034 (mtm) cc_final: 0.7637 (mtm) REVERT: M 126 GLU cc_start: 0.8318 (tp30) cc_final: 0.7604 (tp30) REVERT: M 128 ASN cc_start: 0.8321 (m-40) cc_final: 0.8041 (m-40) REVERT: M 130 LEU cc_start: 0.8494 (tp) cc_final: 0.8106 (tp) REVERT: M 134 ILE cc_start: 0.8310 (mt) cc_final: 0.8087 (tp) REVERT: M 135 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8391 (mmtt) REVERT: M 152 ASN cc_start: 0.8001 (m-40) cc_final: 0.7736 (m-40) REVERT: M 161 GLN cc_start: 0.8351 (tp40) cc_final: 0.8120 (tp-100) REVERT: M 172 VAL cc_start: 0.8779 (t) cc_final: 0.8440 (t) REVERT: M 180 TYR cc_start: 0.6770 (m-10) cc_final: 0.6328 (m-10) REVERT: M 201 GLU cc_start: 0.5695 (tm-30) cc_final: 0.4722 (tm-30) REVERT: M 203 GLN cc_start: 0.7211 (mm110) cc_final: 0.6772 (mm-40) REVERT: M 209 CYS cc_start: 0.7403 (t) cc_final: 0.6515 (m) REVERT: M 220 LEU cc_start: 0.8237 (mm) cc_final: 0.7833 (mm) REVERT: M 234 HIS cc_start: 0.8118 (t-90) cc_final: 0.7698 (t-90) REVERT: M 242 TRP cc_start: 0.7883 (t-100) cc_final: 0.7286 (t-100) REVERT: M 245 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6206 (mm-30) REVERT: M 257 PHE cc_start: 0.8209 (p90) cc_final: 0.7825 (p90) REVERT: M 258 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7819 (mtm180) REVERT: M 262 TYR cc_start: 0.8339 (p90) cc_final: 0.8074 (p90) REVERT: M 298 LYS cc_start: 0.9045 (tttt) cc_final: 0.8636 (tttt) REVERT: M 377 PHE cc_start: 0.7821 (p90) cc_final: 0.7563 (p90) REVERT: M 393 ASP cc_start: 0.7665 (t0) cc_final: 0.7321 (t0) REVERT: M 400 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8683 (mmtt) REVERT: M 414 PHE cc_start: 0.7802 (t80) cc_final: 0.7167 (t80) REVERT: C 23 VAL cc_start: 0.8770 (m) cc_final: 0.8343 (m) REVERT: C 44 THR cc_start: 0.9108 (m) cc_final: 0.8653 (p) REVERT: C 57 GLU cc_start: 0.7996 (tt0) cc_final: 0.7576 (tt0) REVERT: C 68 VAL cc_start: 0.8108 (t) cc_final: 0.7879 (p) REVERT: C 78 TRP cc_start: 0.8309 (m-10) cc_final: 0.7915 (m-10) REVERT: C 81 TYR cc_start: 0.7166 (m-80) cc_final: 0.6462 (m-80) REVERT: C 82 PHE cc_start: 0.8159 (m-80) cc_final: 0.7390 (m-80) REVERT: C 84 ASN cc_start: 0.8485 (t0) cc_final: 0.7773 (t0) REVERT: C 95 ASN cc_start: 0.7778 (t0) cc_final: 0.7429 (t0) REVERT: C 115 GLU cc_start: 0.8021 (tt0) cc_final: 0.7739 (tt0) REVERT: C 117 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8275 (ttp-110) REVERT: C 138 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7078 (mt-10) REVERT: C 168 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 171 ASP cc_start: 0.8117 (m-30) cc_final: 0.7620 (m-30) REVERT: Y 411 HIS cc_start: 0.4813 (t-90) cc_final: 0.4495 (t70) REVERT: b 43 LYS cc_start: 0.8072 (mttt) cc_final: 0.7637 (tptm) REVERT: b 47 LEU cc_start: 0.9037 (mt) cc_final: 0.8650 (mt) REVERT: b 48 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8329 (ptpp) REVERT: b 50 MET cc_start: 0.8218 (mtm) cc_final: 0.7916 (mtm) REVERT: b 52 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7893 (mm-30) REVERT: b 54 ASN cc_start: 0.8043 (m110) cc_final: 0.7700 (m-40) REVERT: b 63 MET cc_start: 0.8747 (mmm) cc_final: 0.8037 (mmm) REVERT: b 66 ILE cc_start: 0.8345 (mp) cc_final: 0.8009 (mp) REVERT: b 72 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8444 (mmtt) REVERT: b 80 PHE cc_start: 0.8438 (t80) cc_final: 0.8047 (t80) REVERT: b 83 VAL cc_start: 0.8337 (t) cc_final: 0.8065 (t) REVERT: b 91 ASN cc_start: 0.7227 (t0) cc_final: 0.6347 (t0) REVERT: b 101 TYR cc_start: 0.8811 (t80) cc_final: 0.8600 (t80) REVERT: b 107 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7467 (mt-10) REVERT: b 112 LEU cc_start: 0.8261 (mp) cc_final: 0.7604 (mp) REVERT: b 121 GLN cc_start: 0.8085 (tt0) cc_final: 0.7845 (mt0) REVERT: b 124 LEU cc_start: 0.8887 (tp) cc_final: 0.8673 (tt) REVERT: b 128 ASN cc_start: 0.8139 (t0) cc_final: 0.7721 (t0) REVERT: b 132 ARG cc_start: 0.8373 (mtt180) cc_final: 0.8123 (mtm180) REVERT: b 147 ILE cc_start: 0.8321 (pt) cc_final: 0.7610 (pt) REVERT: b 150 ILE cc_start: 0.8286 (mt) cc_final: 0.8067 (mt) REVERT: b 151 MET cc_start: 0.7630 (mtp) cc_final: 0.6996 (mtp) REVERT: b 152 MET cc_start: 0.8034 (tpt) cc_final: 0.7787 (tpt) REVERT: b 162 LEU cc_start: 0.7953 (mp) cc_final: 0.7145 (tp) REVERT: b 190 GLU cc_start: 0.7959 (tt0) cc_final: 0.7659 (tt0) REVERT: b 195 LEU cc_start: 0.9016 (mt) cc_final: 0.8745 (tt) REVERT: b 199 LYS cc_start: 0.8062 (mppt) cc_final: 0.7822 (mmtm) REVERT: b 209 MET cc_start: 0.7561 (tmm) cc_final: 0.7321 (tmm) REVERT: b 212 GLU cc_start: 0.8145 (tp30) cc_final: 0.7721 (tp30) REVERT: b 215 CYS cc_start: 0.8938 (m) cc_final: 0.8370 (p) REVERT: b 225 ASN cc_start: 0.8093 (m-40) cc_final: 0.7214 (m-40) REVERT: b 228 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8302 (ttpt) REVERT: b 237 GLU cc_start: 0.7586 (tt0) cc_final: 0.7154 (tt0) REVERT: b 241 GLN cc_start: 0.7990 (mt0) cc_final: 0.7524 (mt0) REVERT: b 302 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8563 (ttm-80) REVERT: b 307 LEU cc_start: 0.8859 (mt) cc_final: 0.8454 (mt) REVERT: b 308 LEU cc_start: 0.8844 (mt) cc_final: 0.8526 (mm) REVERT: b 311 ARG cc_start: 0.8243 (ptt180) cc_final: 0.7724 (ptt-90) REVERT: b 317 MET cc_start: 0.8594 (tpp) cc_final: 0.8269 (tpp) REVERT: b 321 GLN cc_start: 0.7956 (tt0) cc_final: 0.7266 (tt0) REVERT: b 324 TRP cc_start: 0.8585 (t-100) cc_final: 0.8114 (t-100) REVERT: b 326 ILE cc_start: 0.7884 (mm) cc_final: 0.7630 (mm) REVERT: b 341 ARG cc_start: 0.8625 (ptt90) cc_final: 0.8203 (ptm-80) REVERT: b 346 ASN cc_start: 0.7332 (p0) cc_final: 0.6791 (p0) REVERT: b 360 MET cc_start: 0.7938 (tpp) cc_final: 0.6596 (tpp) REVERT: b 363 GLN cc_start: 0.8991 (mp10) cc_final: 0.8718 (mp10) REVERT: b 384 MET cc_start: 0.7939 (ptt) cc_final: 0.7435 (ptt) REVERT: b 386 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8257 (mtpt) REVERT: b 391 GLU cc_start: 0.8183 (tp30) cc_final: 0.7966 (tp30) REVERT: b 417 ASP cc_start: 0.7804 (t0) cc_final: 0.7495 (t0) REVERT: b 629 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7853 (ttmm) REVERT: b 631 THR cc_start: 0.8972 (m) cc_final: 0.8758 (t) REVERT: b 640 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: m 17 GLU cc_start: 0.7566 (pt0) cc_final: 0.7266 (pt0) REVERT: m 21 LYS cc_start: 0.8017 (mttt) cc_final: 0.7529 (mttm) REVERT: m 29 CYS cc_start: 0.8532 (m) cc_final: 0.7858 (t) REVERT: m 36 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7979 (tp-100) REVERT: m 43 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7461 (mt-10) REVERT: m 44 ASN cc_start: 0.8347 (t0) cc_final: 0.7583 (t0) REVERT: m 45 VAL cc_start: 0.8887 (t) cc_final: 0.8659 (t) REVERT: m 71 GLN cc_start: 0.8319 (tp40) cc_final: 0.7928 (tp40) REVERT: m 72 THR cc_start: 0.8590 (p) cc_final: 0.8339 (p) REVERT: m 80 ILE cc_start: 0.8587 (mt) cc_final: 0.8339 (mm) REVERT: m 88 ASP cc_start: 0.8327 (m-30) cc_final: 0.8049 (m-30) REVERT: m 108 ILE cc_start: 0.8960 (mt) cc_final: 0.8580 (mm) REVERT: m 116 MET cc_start: 0.7692 (mtm) cc_final: 0.7411 (mtm) REVERT: m 126 GLU cc_start: 0.8333 (tp30) cc_final: 0.7625 (tp30) REVERT: m 128 ASN cc_start: 0.8120 (m-40) cc_final: 0.7576 (m-40) REVERT: m 129 ILE cc_start: 0.8915 (mm) cc_final: 0.8633 (tp) REVERT: m 131 LYS cc_start: 0.8594 (mttp) cc_final: 0.7732 (mtmm) REVERT: m 140 LEU cc_start: 0.8467 (mt) cc_final: 0.8200 (tt) REVERT: m 141 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7642 (mmt90) REVERT: m 161 GLN cc_start: 0.8295 (tp40) cc_final: 0.8016 (tp-100) REVERT: m 203 GLN cc_start: 0.7086 (mm110) cc_final: 0.6810 (mm-40) REVERT: m 209 CYS cc_start: 0.7442 (t) cc_final: 0.6404 (m) REVERT: m 220 LEU cc_start: 0.8192 (mm) cc_final: 0.7909 (mm) REVERT: m 240 LYS cc_start: 0.8620 (mttt) cc_final: 0.7875 (mmmm) REVERT: m 243 GLU cc_start: 0.8589 (tp30) cc_final: 0.8265 (tp30) REVERT: m 257 PHE cc_start: 0.8547 (p90) cc_final: 0.8151 (p90) REVERT: m 258 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8098 (mtm180) REVERT: m 262 TYR cc_start: 0.8167 (p90) cc_final: 0.6972 (p90) REVERT: m 272 ILE cc_start: 0.8142 (mm) cc_final: 0.7679 (tp) REVERT: m 387 LEU cc_start: 0.8682 (tp) cc_final: 0.7938 (pt) REVERT: m 393 ASP cc_start: 0.8049 (t0) cc_final: 0.7560 (t0) REVERT: m 400 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8700 (mmtt) REVERT: m 402 PHE cc_start: 0.7753 (m-80) cc_final: 0.7356 (m-10) REVERT: m 403 LYS cc_start: 0.7717 (mptt) cc_final: 0.7248 (mptt) REVERT: m 406 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8507 (ttpt) REVERT: m 407 TYR cc_start: 0.8650 (m-80) cc_final: 0.8123 (m-80) REVERT: m 414 PHE cc_start: 0.7822 (t80) cc_final: 0.7555 (t80) REVERT: c 53 VAL cc_start: 0.8671 (t) cc_final: 0.8430 (m) REVERT: c 64 THR cc_start: 0.6515 (m) cc_final: 0.6237 (t) REVERT: c 78 TRP cc_start: 0.8352 (m-10) cc_final: 0.7497 (m-10) REVERT: c 82 PHE cc_start: 0.8025 (m-10) cc_final: 0.7725 (m-80) REVERT: c 84 ASN cc_start: 0.8466 (t0) cc_final: 0.7641 (t0) REVERT: c 95 ASN cc_start: 0.7688 (t160) cc_final: 0.7452 (t160) REVERT: c 97 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7674 (mmm-85) REVERT: c 110 MET cc_start: 0.8447 (mmm) cc_final: 0.7800 (mmm) REVERT: c 115 GLU cc_start: 0.7847 (tt0) cc_final: 0.7492 (tt0) REVERT: c 171 ASP cc_start: 0.7951 (m-30) cc_final: 0.7526 (m-30) REVERT: y 415 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7521 (mm110) outliers start: 0 outliers final: 0 residues processed: 762 average time/residue: 0.3103 time to fit residues: 333.9885 Evaluate side-chains 752 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 752 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 137 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 355 GLN M 54 HIS M 128 ASN b 231 ASN b 355 GLN m 26 GLN m 54 HIS m 380 GLN c 95 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111346 restraints weight = 30788.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115629 restraints weight = 16769.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118623 restraints weight = 10514.195| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16108 Z= 0.214 Angle : 0.607 7.847 21822 Z= 0.317 Chirality : 0.046 0.173 2524 Planarity : 0.005 0.048 2752 Dihedral : 9.226 158.790 2154 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.01 (0.20), residues: 1954 helix: 1.09 (0.18), residues: 828 sheet: 0.37 (0.28), residues: 378 loop : 0.58 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.003 TRP c 172 HIS 0.005 0.001 HIS b 246 PHE 0.018 0.002 PHE M 78 TYR 0.024 0.002 TYR B 351 ARG 0.010 0.001 ARG C 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6723.18 seconds wall clock time: 122 minutes 22.24 seconds (7342.24 seconds total)