Starting phenix.real_space_refine on Sat Jul 4 12:09:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3o_15831/07_2026/8b3o_15831.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 13485 2.51 5 N 3210 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20475 Number of models: 1 Model: "" Number of chains: 45 Chain: "KKK" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "PPP" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 175 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "UUU" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ZZZ" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 319 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "AAA" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "FFF" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1123 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "eee" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "jjj" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ooo" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "LLL" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "QQQ" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 175 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "VVV" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "aaa" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 319 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "BBB" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "GGG" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1123 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "fff" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "kkk" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ppp" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "MMM" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "RRR" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 175 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "WWW" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "bbb" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 319 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "CCC" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "HHH" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1123 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "ggg" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "lll" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "qqq" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "NNN" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "SSS" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 175 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "XXX" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ccc" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 319 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "DDD" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "III" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1123 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "hhh" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "mmm" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "rrr" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "OOO" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "TTT" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 175 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "YYY" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ddd" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 319 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "EEE" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "JJJ" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1123 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "iii" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "nnn" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "sss" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 4.84, per 1000 atoms: 0.24 Number of scatterers: 20475 At special positions: 0 Unit cell: (84.7924, 83.6912, 262.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 3670 8.00 N 3210 7.00 C 13485 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: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 10 sheets defined 79.4% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'KKK' and resid 16 through 49 removed outlier: 3.570A pdb=" N LEUKKK 41 " --> pdb=" O ILEKKK 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERKKK 47 " --> pdb=" O LYSKKK 43 " (cutoff:3.500A) Processing helix chain 'PPP' and resid 28 through 49 removed outlier: 3.585A pdb=" N LEUPPP 41 " --> pdb=" O ILEPPP 37 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SERPPP 47 " --> pdb=" O LYSPPP 43 " (cutoff:3.500A) Processing helix chain 'UUU' and resid 6 through 49 removed outlier: 3.906A pdb=" N ALAUUU 10 " --> pdb=" O PROUUU 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUUUU 41 " --> pdb=" O ILEUUU 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERUUU 47 " --> pdb=" O LYSUUU 43 " (cutoff:3.500A) Processing helix chain 'ZZZ' and resid 9 through 49 removed outlier: 3.580A pdb=" N LEUZZZ 41 " --> pdb=" O ILEZZZ 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERZZZ 47 " --> pdb=" O LYSZZZ 43 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 6 through 14 removed outlier: 3.557A pdb=" N ARGAAA 12 " --> pdb=" O PROAAA 8 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 16 through 55 removed outlier: 3.729A pdb=" N LEUAAA 26 " --> pdb=" O PHEAAA 22 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILEAAA 36 " --> pdb=" O GLYAAA 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALAAAA 37 " --> pdb=" O PHEAAA 33 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERAAA 52 " --> pdb=" O ILEAAA 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILEAAA 53 " --> pdb=" O GLYAAA 49 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 69 through 74 removed outlier: 4.215A pdb=" N VALAAA 73 " --> pdb=" O PHEAAA 69 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 80 through 105 removed outlier: 4.057A pdb=" N LYSAAA 92 " --> pdb=" O ILEAAA 88 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALAAAA 93 " --> pdb=" O LEUAAA 89 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VALAAA 105 " --> pdb=" O LYSAAA 101 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 106 through 110 Processing helix chain 'FFF' and resid 259 through 268 removed outlier: 3.577A pdb=" N ALAFFF 264 " --> pdb=" O TYRFFF 260 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASNFFF 265 " --> pdb=" O GLUFFF 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALAFFF 266 " --> pdb=" O LYSFFF 262 " (cutoff:3.500A) Processing helix chain 'FFF' and resid 269 through 271 No H-bonds generated for 'chain 'FFF' and resid 269 through 271' Processing helix chain 'FFF' and resid 276 through 289 removed outlier: 4.355A pdb=" N SERFFF 282 " --> pdb=" O ASNFFF 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPFFF 283 " --> pdb=" O ALAFFF 279 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALAFFF 284 " --> pdb=" O LEUFFF 280 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYSFFF 285 " --> pdb=" O GLNFFF 281 " (cutoff:3.500A) Processing helix chain 'FFF' and resid 291 through 303 Processing helix chain 'FFF' and resid 325 through 330 removed outlier: 3.689A pdb=" N VALFFF 329 " --> pdb=" O GLNFFF 325 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLYFFF 330 " --> pdb=" O METFFF 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'FFF' and resid 325 through 330' Processing helix chain 'FFF' and resid 374 through 399 removed outlier: 3.604A pdb=" N PHEFFF 383 " --> pdb=" O GLYFFF 379 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALAFFF 388 " --> pdb=" O LEUFFF 384 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYRFFF 392 " --> pdb=" O ALAFFF 388 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SERFFF 395 " --> pdb=" O METFFF 391 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASNFFF 399 " --> pdb=" O SERFFF 395 " (cutoff:3.500A) Processing helix chain 'eee' and resid 6 through 47 removed outlier: 3.972A pdb=" N ALAeee 10 " --> pdb=" O PROeee 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAeee 27 " --> pdb=" O GLYeee 23 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALeee 30 " --> pdb=" O TRPeee 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALeee 31 " --> pdb=" O ALAeee 27 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHEeee 42 " --> pdb=" O GLYeee 38 " (cutoff:3.500A) Processing helix chain 'jjj' and resid 6 through 50 Processing helix chain 'ooo' and resid 6 through 49 removed outlier: 3.905A pdb=" N ALAooo 10 " --> pdb=" O PROooo 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUooo 41 " --> pdb=" O ILEooo 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERooo 47 " --> pdb=" O LYSooo 43 " (cutoff:3.500A) Processing helix chain 'LLL' and resid 17 through 49 removed outlier: 3.570A pdb=" N LEULLL 41 " --> pdb=" O ILELLL 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERLLL 47 " --> pdb=" O LYSLLL 43 " (cutoff:3.500A) Processing helix chain 'QQQ' and resid 28 through 49 removed outlier: 3.584A pdb=" N LEUQQQ 41 " --> pdb=" O ILEQQQ 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SERQQQ 47 " --> pdb=" O LYSQQQ 43 " (cutoff:3.500A) Processing helix chain 'VVV' and resid 6 through 49 removed outlier: 3.905A pdb=" N ALAVVV 10 " --> pdb=" O PROVVV 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUVVV 41 " --> pdb=" O ILEVVV 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SERVVV 47 " --> pdb=" O LYSVVV 43 " (cutoff:3.500A) Processing helix chain 'aaa' and resid 9 through 49 removed outlier: 3.583A pdb=" N LEUaaa 41 " --> pdb=" O ILEaaa 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERaaa 47 " --> pdb=" O LYSaaa 43 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 6 through 14 removed outlier: 3.559A pdb=" N ARGBBB 12 " --> pdb=" O PROBBB 8 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 16 through 55 removed outlier: 3.729A pdb=" N LEUBBB 26 " --> pdb=" O PHEBBB 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEBBB 36 " --> pdb=" O GLYBBB 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALABBB 37 " --> pdb=" O PHEBBB 33 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERBBB 52 " --> pdb=" O ILEBBB 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILEBBB 53 " --> pdb=" O GLYBBB 49 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 69 through 74 removed outlier: 4.211A pdb=" N VALBBB 73 " --> pdb=" O PHEBBB 69 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 80 through 105 removed outlier: 4.056A pdb=" N LYSBBB 92 " --> pdb=" O ILEBBB 88 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALABBB 93 " --> pdb=" O LEUBBB 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VALBBB 105 " --> pdb=" O LYSBBB 101 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 106 through 110 Processing helix chain 'GGG' and resid 259 through 268 removed outlier: 3.578A pdb=" N ALAGGG 264 " --> pdb=" O TYRGGG 260 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASNGGG 265 " --> pdb=" O GLUGGG 261 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAGGG 266 " --> pdb=" O LYSGGG 262 " (cutoff:3.500A) Processing helix chain 'GGG' and resid 269 through 271 No H-bonds generated for 'chain 'GGG' and resid 269 through 271' Processing helix chain 'GGG' and resid 276 through 289 removed outlier: 4.355A pdb=" N SERGGG 282 " --> pdb=" O ASNGGG 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPGGG 283 " --> pdb=" O ALAGGG 279 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALAGGG 284 " --> pdb=" O LEUGGG 280 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYSGGG 285 " --> pdb=" O GLNGGG 281 " (cutoff:3.500A) Processing helix chain 'GGG' and resid 291 through 303 Processing helix chain 'GGG' and resid 325 through 330 removed outlier: 3.689A pdb=" N VALGGG 329 " --> pdb=" O GLNGGG 325 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLYGGG 330 " --> pdb=" O METGGG 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'GGG' and resid 325 through 330' Processing helix chain 'GGG' and resid 339 through 343 removed outlier: 3.616A pdb=" N ARGGGG 342 " --> pdb=" O ASNGGG 339 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLNGGG 343 " --> pdb=" O ASNGGG 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'GGG' and resid 339 through 343' Processing helix chain 'GGG' and resid 374 through 399 removed outlier: 3.604A pdb=" N PHEGGG 383 " --> pdb=" O GLYGGG 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALAGGG 388 " --> pdb=" O LEUGGG 384 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYRGGG 392 " --> pdb=" O ALAGGG 388 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SERGGG 395 " --> pdb=" O METGGG 391 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASNGGG 399 " --> pdb=" O SERGGG 395 " (cutoff:3.500A) Processing helix chain 'fff' and resid 6 through 47 removed outlier: 3.972A pdb=" N ALAfff 10 " --> pdb=" O PROfff 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAfff 27 " --> pdb=" O GLYfff 23 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VALfff 30 " --> pdb=" O TRPfff 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALfff 31 " --> pdb=" O ALAfff 27 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHEfff 42 " --> pdb=" O GLYfff 38 " (cutoff:3.500A) Processing helix chain 'kkk' and resid 6 through 50 Processing helix chain 'ppp' and resid 6 through 49 removed outlier: 3.910A pdb=" N ALAppp 10 " --> pdb=" O PROppp 6 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEUppp 41 " --> pdb=" O ILEppp 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERppp 47 " --> pdb=" O LYSppp 43 " (cutoff:3.500A) Processing helix chain 'MMM' and resid 17 through 49 removed outlier: 3.571A pdb=" N LEUMMM 41 " --> pdb=" O ILEMMM 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SERMMM 47 " --> pdb=" O LYSMMM 43 " (cutoff:3.500A) Processing helix chain 'RRR' and resid 28 through 49 removed outlier: 3.584A pdb=" N LEURRR 41 " --> pdb=" O ILERRR 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERRRR 47 " --> pdb=" O LYSRRR 43 " (cutoff:3.500A) Processing helix chain 'WWW' and resid 6 through 49 removed outlier: 3.905A pdb=" N ALAWWW 10 " --> pdb=" O PROWWW 6 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEUWWW 41 " --> pdb=" O ILEWWW 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERWWW 47 " --> pdb=" O LYSWWW 43 " (cutoff:3.500A) Processing helix chain 'bbb' and resid 9 through 49 removed outlier: 3.580A pdb=" N LEUbbb 41 " --> pdb=" O ILEbbb 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERbbb 47 " --> pdb=" O LYSbbb 43 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 6 through 14 removed outlier: 3.559A pdb=" N ARGCCC 12 " --> pdb=" O PROCCC 8 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 16 through 55 removed outlier: 3.730A pdb=" N LEUCCC 26 " --> pdb=" O PHECCC 22 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILECCC 36 " --> pdb=" O GLYCCC 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALACCC 37 " --> pdb=" O PHECCC 33 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERCCC 52 " --> pdb=" O ILECCC 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILECCC 53 " --> pdb=" O GLYCCC 49 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 69 through 74 removed outlier: 4.214A pdb=" N VALCCC 73 " --> pdb=" O PHECCC 69 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 80 through 105 removed outlier: 4.055A pdb=" N LYSCCC 92 " --> pdb=" O ILECCC 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALACCC 93 " --> pdb=" O LEUCCC 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VALCCC 105 " --> pdb=" O LYSCCC 101 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 106 through 110 Processing helix chain 'HHH' and resid 259 through 268 removed outlier: 3.575A pdb=" N ALAHHH 264 " --> pdb=" O TYRHHH 260 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASNHHH 265 " --> pdb=" O GLUHHH 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAHHH 266 " --> pdb=" O LYSHHH 262 " (cutoff:3.500A) Processing helix chain 'HHH' and resid 269 through 271 No H-bonds generated for 'chain 'HHH' and resid 269 through 271' Processing helix chain 'HHH' and resid 276 through 289 removed outlier: 4.355A pdb=" N SERHHH 282 " --> pdb=" O ASNHHH 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPHHH 283 " --> pdb=" O ALAHHH 279 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALAHHH 284 " --> pdb=" O LEUHHH 280 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYSHHH 285 " --> pdb=" O GLNHHH 281 " (cutoff:3.500A) Processing helix chain 'HHH' and resid 291 through 303 Processing helix chain 'HHH' and resid 325 through 330 removed outlier: 3.689A pdb=" N VALHHH 329 " --> pdb=" O GLNHHH 325 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLYHHH 330 " --> pdb=" O METHHH 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'HHH' and resid 325 through 330' Processing helix chain 'HHH' and resid 339 through 343 removed outlier: 3.616A pdb=" N ARGHHH 342 " --> pdb=" O ASNHHH 339 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLNHHH 343 " --> pdb=" O ASNHHH 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'HHH' and resid 339 through 343' Processing helix chain 'HHH' and resid 374 through 399 removed outlier: 3.605A pdb=" N PHEHHH 383 " --> pdb=" O GLYHHH 379 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALAHHH 388 " --> pdb=" O LEUHHH 384 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYRHHH 392 " --> pdb=" O ALAHHH 388 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SERHHH 395 " --> pdb=" O METHHH 391 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASNHHH 399 " --> pdb=" O SERHHH 395 " (cutoff:3.500A) Processing helix chain 'ggg' and resid 6 through 47 removed outlier: 3.974A pdb=" N ALAggg 10 " --> pdb=" O PROggg 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAggg 27 " --> pdb=" O GLYggg 23 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VALggg 30 " --> pdb=" O TRPggg 26 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VALggg 31 " --> pdb=" O ALAggg 27 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHEggg 42 " --> pdb=" O GLYggg 38 " (cutoff:3.500A) Processing helix chain 'lll' and resid 6 through 50 Processing helix chain 'qqq' and resid 6 through 49 removed outlier: 3.909A pdb=" N ALAqqq 10 " --> pdb=" O PROqqq 6 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEUqqq 41 " --> pdb=" O ILEqqq 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SERqqq 47 " --> pdb=" O LYSqqq 43 " (cutoff:3.500A) Processing helix chain 'NNN' and resid 17 through 49 removed outlier: 3.571A pdb=" N LEUNNN 41 " --> pdb=" O ILENNN 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SERNNN 47 " --> pdb=" O LYSNNN 43 " (cutoff:3.500A) Processing helix chain 'SSS' and resid 28 through 49 removed outlier: 3.585A pdb=" N LEUSSS 41 " --> pdb=" O ILESSS 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERSSS 47 " --> pdb=" O LYSSSS 43 " (cutoff:3.500A) Processing helix chain 'XXX' and resid 6 through 49 removed outlier: 3.906A pdb=" N ALAXXX 10 " --> pdb=" O PROXXX 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUXXX 41 " --> pdb=" O ILEXXX 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SERXXX 47 " --> pdb=" O LYSXXX 43 " (cutoff:3.500A) Processing helix chain 'ccc' and resid 9 through 49 removed outlier: 3.580A pdb=" N LEUccc 41 " --> pdb=" O ILEccc 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SERccc 47 " --> pdb=" O LYSccc 43 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 6 through 14 removed outlier: 3.559A pdb=" N ARGDDD 12 " --> pdb=" O PRODDD 8 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 16 through 55 removed outlier: 3.730A pdb=" N LEUDDD 26 " --> pdb=" O PHEDDD 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILEDDD 36 " --> pdb=" O GLYDDD 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALADDD 37 " --> pdb=" O PHEDDD 33 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERDDD 52 " --> pdb=" O ILEDDD 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEDDD 53 " --> pdb=" O GLYDDD 49 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 69 through 74 removed outlier: 4.218A pdb=" N VALDDD 73 " --> pdb=" O PHEDDD 69 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 80 through 105 removed outlier: 4.057A pdb=" N LYSDDD 92 " --> pdb=" O ILEDDD 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALADDD 93 " --> pdb=" O LEUDDD 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VALDDD 105 " --> pdb=" O LYSDDD 101 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 106 through 110 Processing helix chain 'III' and resid 259 through 268 removed outlier: 3.575A pdb=" N ALAIII 264 " --> pdb=" O TYRIII 260 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASNIII 265 " --> pdb=" O GLUIII 261 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALAIII 266 " --> pdb=" O LYSIII 262 " (cutoff:3.500A) Processing helix chain 'III' and resid 269 through 271 No H-bonds generated for 'chain 'III' and resid 269 through 271' Processing helix chain 'III' and resid 276 through 289 removed outlier: 4.353A pdb=" N SERIII 282 " --> pdb=" O ASNIII 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPIII 283 " --> pdb=" O ALAIII 279 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALAIII 284 " --> pdb=" O LEUIII 280 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYSIII 285 " --> pdb=" O GLNIII 281 " (cutoff:3.500A) Processing helix chain 'III' and resid 291 through 303 Processing helix chain 'III' and resid 325 through 330 removed outlier: 3.688A pdb=" N VALIII 329 " --> pdb=" O GLNIII 325 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLYIII 330 " --> pdb=" O METIII 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'III' and resid 325 through 330' Processing helix chain 'III' and resid 374 through 399 removed outlier: 3.603A pdb=" N PHEIII 383 " --> pdb=" O GLYIII 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALAIII 388 " --> pdb=" O LEUIII 384 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYRIII 392 " --> pdb=" O ALAIII 388 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SERIII 395 " --> pdb=" O METIII 391 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASNIII 399 " --> pdb=" O SERIII 395 " (cutoff:3.500A) Processing helix chain 'hhh' and resid 6 through 47 removed outlier: 3.975A pdb=" N ALAhhh 10 " --> pdb=" O PROhhh 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAhhh 27 " --> pdb=" O GLYhhh 23 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALhhh 30 " --> pdb=" O TRPhhh 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALhhh 31 " --> pdb=" O ALAhhh 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHEhhh 42 " --> pdb=" O GLYhhh 38 " (cutoff:3.500A) Processing helix chain 'mmm' and resid 6 through 50 Processing helix chain 'rrr' and resid 6 through 49 removed outlier: 3.905A pdb=" N ALArrr 10 " --> pdb=" O PROrrr 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUrrr 41 " --> pdb=" O ILErrr 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERrrr 47 " --> pdb=" O LYSrrr 43 " (cutoff:3.500A) Processing helix chain 'OOO' and resid 17 through 49 removed outlier: 3.576A pdb=" N LEUOOO 41 " --> pdb=" O ILEOOO 37 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SEROOO 47 " --> pdb=" O LYSOOO 43 " (cutoff:3.500A) Processing helix chain 'TTT' and resid 28 through 49 removed outlier: 3.585A pdb=" N LEUTTT 41 " --> pdb=" O ILETTT 37 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SERTTT 47 " --> pdb=" O LYSTTT 43 " (cutoff:3.500A) Processing helix chain 'YYY' and resid 6 through 49 removed outlier: 3.904A pdb=" N ALAYYY 10 " --> pdb=" O PROYYY 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUYYY 41 " --> pdb=" O ILEYYY 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERYYY 47 " --> pdb=" O LYSYYY 43 " (cutoff:3.500A) Processing helix chain 'ddd' and resid 9 through 49 removed outlier: 3.581A pdb=" N LEUddd 41 " --> pdb=" O ILEddd 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SERddd 47 " --> pdb=" O LYSddd 43 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 6 through 14 removed outlier: 3.563A pdb=" N ARGEEE 12 " --> pdb=" O PROEEE 8 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 16 through 55 removed outlier: 3.731A pdb=" N LEUEEE 26 " --> pdb=" O PHEEEE 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEEEE 36 " --> pdb=" O GLYEEE 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALAEEE 37 " --> pdb=" O PHEEEE 33 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SEREEE 52 " --> pdb=" O ILEEEE 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILEEEE 53 " --> pdb=" O GLYEEE 49 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 69 through 74 removed outlier: 4.219A pdb=" N VALEEE 73 " --> pdb=" O PHEEEE 69 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 80 through 105 removed outlier: 4.057A pdb=" N LYSEEE 92 " --> pdb=" O ILEEEE 88 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALAEEE 93 " --> pdb=" O LEUEEE 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VALEEE 105 " --> pdb=" O LYSEEE 101 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 106 through 110 Processing helix chain 'JJJ' and resid 259 through 268 removed outlier: 3.577A pdb=" N ALAJJJ 264 " --> pdb=" O TYRJJJ 260 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASNJJJ 265 " --> pdb=" O GLUJJJ 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALAJJJ 266 " --> pdb=" O LYSJJJ 262 " (cutoff:3.500A) Processing helix chain 'JJJ' and resid 269 through 271 No H-bonds generated for 'chain 'JJJ' and resid 269 through 271' Processing helix chain 'JJJ' and resid 276 through 289 removed outlier: 4.356A pdb=" N SERJJJ 282 " --> pdb=" O ASNJJJ 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPJJJ 283 " --> pdb=" O ALAJJJ 279 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALAJJJ 284 " --> pdb=" O LEUJJJ 280 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYSJJJ 285 " --> pdb=" O GLNJJJ 281 " (cutoff:3.500A) Processing helix chain 'JJJ' and resid 291 through 303 Processing helix chain 'JJJ' and resid 325 through 330 removed outlier: 3.689A pdb=" N VALJJJ 329 " --> pdb=" O GLNJJJ 325 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLYJJJ 330 " --> pdb=" O METJJJ 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJJ' and resid 325 through 330' Processing helix chain 'JJJ' and resid 339 through 343 removed outlier: 3.616A pdb=" N ARGJJJ 342 " --> pdb=" O ASNJJJ 339 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLNJJJ 343 " --> pdb=" O ASNJJJ 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJJ' and resid 339 through 343' Processing helix chain 'JJJ' and resid 374 through 399 removed outlier: 3.604A pdb=" N PHEJJJ 383 " --> pdb=" O GLYJJJ 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALAJJJ 388 " --> pdb=" O LEUJJJ 384 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYRJJJ 392 " --> pdb=" O ALAJJJ 388 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SERJJJ 395 " --> pdb=" O METJJJ 391 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASNJJJ 399 " --> pdb=" O SERJJJ 395 " (cutoff:3.500A) Processing helix chain 'iii' and resid 6 through 47 removed outlier: 3.975A pdb=" N ALAiii 10 " --> pdb=" O PROiii 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAiii 27 " --> pdb=" O GLYiii 23 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALiii 30 " --> pdb=" O TRPiii 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALiii 31 " --> pdb=" O ALAiii 27 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHEiii 42 " --> pdb=" O GLYiii 38 " (cutoff:3.500A) Processing helix chain 'nnn' and resid 6 through 50 Processing helix chain 'sss' and resid 6 through 49 removed outlier: 3.905A pdb=" N ALAsss 10 " --> pdb=" O PROsss 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUsss 41 " --> pdb=" O ILEsss 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERsss 47 " --> pdb=" O LYSsss 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AAA' and resid 2 through 3 removed outlier: 3.651A pdb=" N VALAAA 3 " --> pdb=" O GLUFFF 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'FFF' and resid 357 through 359 removed outlier: 3.629A pdb=" N PHEFFF 357 " --> pdb=" O ILEFFF 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BBB' and resid 2 through 3 removed outlier: 3.640A pdb=" N VALBBB 3 " --> pdb=" O GLUGGG 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'GGG' and resid 357 through 359 removed outlier: 3.629A pdb=" N PHEGGG 357 " --> pdb=" O ILEGGG 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'CCC' and resid 2 through 3 removed outlier: 3.659A pdb=" N VALCCC 3 " --> pdb=" O GLUHHH 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'HHH' and resid 357 through 359 removed outlier: 3.629A pdb=" N PHEHHH 357 " --> pdb=" O ILEHHH 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'DDD' and resid 2 through 3 removed outlier: 3.668A pdb=" N VALDDD 3 " --> pdb=" O GLUIII 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'III' and resid 357 through 359 removed outlier: 3.630A pdb=" N PHEIII 357 " --> pdb=" O ILEIII 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'EEE' and resid 2 through 3 removed outlier: 3.660A pdb=" N VALEEE 3 " --> pdb=" O GLUJJJ 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'JJJ' and resid 357 through 359 removed outlier: 3.630A pdb=" N PHEJJJ 357 " --> pdb=" O ILEJJJ 369 " (cutoff:3.500A) 1611 hydrogen bonds defined for protein. 4773 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: 3.17 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5869 1.34 - 1.46: 5421 1.46 - 1.58: 9365 1.58 - 1.70: 0 1.70 - 1.82: 205 Bond restraints: 20860 Sorted by residual: bond pdb=" C SERFFF 335 " pdb=" O SERFFF 335 " ideal model delta sigma weight residual 1.249 1.227 0.022 8.50e-03 1.38e+04 6.53e+00 bond pdb=" C SERGGG 335 " pdb=" O SERGGG 335 " ideal model delta sigma weight residual 1.249 1.227 0.022 8.50e-03 1.38e+04 6.45e+00 bond pdb=" C SERJJJ 335 " pdb=" O SERJJJ 335 " ideal model delta sigma weight residual 1.249 1.227 0.022 8.50e-03 1.38e+04 6.41e+00 bond pdb=" C SERIII 335 " pdb=" O SERIII 335 " ideal model delta sigma weight residual 1.249 1.228 0.021 8.50e-03 1.38e+04 6.24e+00 bond pdb=" C SERHHH 335 " pdb=" O SERHHH 335 " ideal model delta sigma weight residual 1.249 1.228 0.021 8.50e-03 1.38e+04 6.09e+00 ... (remaining 20855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 24621 2.12 - 4.23: 3318 4.23 - 6.35: 177 6.35 - 8.47: 24 8.47 - 10.59: 5 Bond angle restraints: 28145 Sorted by residual: angle pdb=" C THRfff 46 " pdb=" CA THRfff 46 " pdb=" CB THRfff 46 " ideal model delta sigma weight residual 109.24 119.83 -10.59 1.75e+00 3.27e-01 3.66e+01 angle pdb=" C THRhhh 46 " pdb=" CA THRhhh 46 " pdb=" CB THRhhh 46 " ideal model delta sigma weight residual 109.24 119.77 -10.53 1.75e+00 3.27e-01 3.62e+01 angle pdb=" C THRiii 46 " pdb=" CA THRiii 46 " pdb=" CB THRiii 46 " ideal model delta sigma weight residual 109.24 119.75 -10.51 1.75e+00 3.27e-01 3.61e+01 angle pdb=" C THRggg 46 " pdb=" CA THRggg 46 " pdb=" CB THRggg 46 " ideal model delta sigma weight residual 109.24 119.66 -10.42 1.75e+00 3.27e-01 3.55e+01 angle pdb=" C THReee 46 " pdb=" CA THReee 46 " pdb=" CB THReee 46 " ideal model delta sigma weight residual 109.24 119.66 -10.42 1.75e+00 3.27e-01 3.55e+01 ... (remaining 28140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 10642 15.58 - 31.16: 1159 31.16 - 46.73: 310 46.73 - 62.31: 139 62.31 - 77.89: 15 Dihedral angle restraints: 12265 sinusoidal: 4500 harmonic: 7765 Sorted by residual: dihedral pdb=" C PHEfff 42 " pdb=" N PHEfff 42 " pdb=" CA PHEfff 42 " pdb=" CB PHEfff 42 " ideal model delta harmonic sigma weight residual -122.60 -134.24 11.64 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" C PHEhhh 42 " pdb=" N PHEhhh 42 " pdb=" CA PHEhhh 42 " pdb=" CB PHEhhh 42 " ideal model delta harmonic sigma weight residual -122.60 -134.22 11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" C THRfff 46 " pdb=" N THRfff 46 " pdb=" CA THRfff 46 " pdb=" CB THRfff 46 " ideal model delta harmonic sigma weight residual -122.00 -133.50 11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 12262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2115 0.083 - 0.167: 1023 0.167 - 0.250: 140 0.250 - 0.333: 32 0.333 - 0.416: 10 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA PHEfff 42 " pdb=" N PHEfff 42 " pdb=" C PHEfff 42 " pdb=" CB PHEfff 42 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA PHEhhh 42 " pdb=" N PHEhhh 42 " pdb=" C PHEhhh 42 " pdb=" CB PHEhhh 42 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA PHEiii 42 " pdb=" N PHEiii 42 " pdb=" C PHEiii 42 " pdb=" CB PHEiii 42 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 3317 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILElll 37 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILElll 37 " 0.029 2.00e-02 2.50e+03 pdb=" O ILElll 37 " -0.011 2.00e-02 2.50e+03 pdb=" N GLYlll 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILEkkk 37 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ILEkkk 37 " 0.029 2.00e-02 2.50e+03 pdb=" O ILEkkk 37 " -0.011 2.00e-02 2.50e+03 pdb=" N GLYkkk 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILEjjj 37 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C ILEjjj 37 " 0.029 2.00e-02 2.50e+03 pdb=" O ILEjjj 37 " -0.011 2.00e-02 2.50e+03 pdb=" N GLYjjj 38 " -0.010 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 7821 2.90 - 3.40: 19059 3.40 - 3.90: 30596 3.90 - 4.40: 36578 4.40 - 4.90: 60563 Nonbonded interactions: 154617 Sorted by model distance: nonbonded pdb=" O ASPFFF 289 " pdb=" OD1 ASPFFF 289 " model vdw 2.406 3.040 nonbonded pdb=" O ASPJJJ 289 " pdb=" OD1 ASPJJJ 289 " model vdw 2.414 3.040 nonbonded pdb=" O ASPGGG 289 " pdb=" OD1 ASPGGG 289 " model vdw 2.417 3.040 nonbonded pdb=" O VALFFF 329 " pdb=" OG SERFFF 335 " model vdw 2.422 3.040 nonbonded pdb=" O VALJJJ 329 " pdb=" OG SERJJJ 335 " model vdw 2.423 3.040 ... (remaining 154612 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'AAA') selection = (chain 'BBB') selection = (chain 'CCC') selection = (chain 'DDD') selection = (chain 'EEE') } ncs_group { reference = (chain 'FFF') selection = (chain 'GGG') selection = (chain 'HHH') selection = (chain 'III') selection = (chain 'JJJ') } ncs_group { reference = (chain 'KKK') selection = (chain 'LLL') selection = (chain 'MMM') selection = (chain 'NNN') selection = (chain 'OOO') } ncs_group { reference = (chain 'PPP') selection = (chain 'QQQ') selection = (chain 'RRR') selection = (chain 'SSS') selection = (chain 'TTT') } ncs_group { reference = (chain 'UUU' and resid 8 through 48) selection = (chain 'VVV' and resid 8 through 48) selection = (chain 'WWW' and resid 8 through 48) selection = (chain 'XXX' and resid 8 through 48) selection = (chain 'YYY' and resid 8 through 48) selection = (chain 'ZZZ' and resid 8 through 48) selection = (chain 'aaa' and resid 8 through 48) selection = (chain 'bbb' and resid 8 through 48) selection = (chain 'ccc' and resid 8 through 48) selection = (chain 'ddd' and resid 8 through 48) selection = (chain 'eee' and resid 8 through 48) selection = (chain 'fff' and resid 8 through 48) selection = (chain 'ggg' and resid 8 through 48) selection = (chain 'hhh' and resid 8 through 48) selection = (chain 'iii' and resid 8 through 48) selection = (chain 'jjj' and resid 8 through 48) selection = (chain 'kkk' and resid 8 through 48) selection = (chain 'lll' and resid 8 through 48) selection = (chain 'mmm' and resid 8 through 48) selection = (chain 'nnn' and resid 8 through 48) selection = (chain 'ooo' and resid 8 through 48) selection = (chain 'ppp' and resid 8 through 48) selection = (chain 'qqq' and resid 8 through 48) selection = (chain 'rrr' and resid 8 through 48) selection = (chain 'sss' and resid 8 through 48) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.680 Find NCS groups from input model: 0.440 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 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 : 0.007 0.040 20860 Z= 0.468 Angle : 1.443 10.586 28145 Z= 1.009 Chirality : 0.091 0.416 3320 Planarity : 0.005 0.017 3430 Dihedral : 15.412 77.890 7255 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.33 % Allowed : 10.12 % Favored : 85.55 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.13), residues: 2630 helix: -2.24 (0.09), residues: 2160 sheet: None (None), residues: 0 loop : -3.13 (0.22), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAAA 12 TYR 0.014 0.003 TYRUUU 24 PHE 0.020 0.003 PHEJJJ 377 TRP 0.008 0.001 TRPDDD 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.47 (20860) covalent geometry : angle 1.44256 / 1.01 (28145) hydrogen bonds : bond 0.34004 / 22.16 ( 1611) hydrogen bonds : angle 8.50092 / 5.92 ( 4773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 717 time to evaluate : 0.774 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: KKK 17 SER cc_start: 0.8497 (m) cc_final: 0.8064 (p) REVERT: KKK 19 THR cc_start: 0.9693 (m) cc_final: 0.9483 (p) REVERT: KKK 44 LYS cc_start: 0.9509 (ttpt) cc_final: 0.9271 (ttmt) REVERT: PPP 40 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9121 (ttpt) REVERT: ZZZ 15 GLN cc_start: 0.9456 (tt0) cc_final: 0.9142 (mt0) REVERT: ZZZ 40 LYS cc_start: 0.9292 (ttmt) cc_final: 0.9060 (ttmt) REVERT: eee 12 ASP cc_start: 0.9068 (m-30) cc_final: 0.8802 (m-30) REVERT: eee 28 MET cc_start: 0.9004 (ttt) cc_final: 0.8801 (ttm) REVERT: jjj 8 LYS cc_start: 0.9393 (ttpt) cc_final: 0.9124 (ttpp) REVERT: jjj 12 ASP cc_start: 0.9059 (m-30) cc_final: 0.8840 (m-30) REVERT: LLL 19 THR cc_start: 0.9669 (m) cc_final: 0.9412 (p) REVERT: LLL 24 TYR cc_start: 0.9550 (m-10) cc_final: 0.9337 (m-10) REVERT: LLL 39 ILE cc_start: 0.9555 (mt) cc_final: 0.9165 (mm) REVERT: LLL 43 LYS cc_start: 0.9583 (mtpt) cc_final: 0.9376 (mtpp) REVERT: LLL 44 LYS cc_start: 0.9543 (ttpt) cc_final: 0.9324 (ttmt) REVERT: QQQ 39 ILE cc_start: 0.9600 (mt) cc_final: 0.9365 (mm) REVERT: QQQ 40 LYS cc_start: 0.9390 (ttmt) cc_final: 0.8981 (ttpt) REVERT: QQQ 41 LEU cc_start: 0.9768 (mt) cc_final: 0.9268 (mp) REVERT: QQQ 45 PHE cc_start: 0.9540 (m-80) cc_final: 0.8971 (m-80) REVERT: aaa 15 GLN cc_start: 0.9468 (tt0) cc_final: 0.9174 (mt0) REVERT: aaa 21 MET cc_start: 0.9668 (mtp) cc_final: 0.9429 (ttp) REVERT: GGG 267 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9073 (m-40) REVERT: GGG 376 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9128 (tt) REVERT: kkk 12 ASP cc_start: 0.9156 (m-30) cc_final: 0.8952 (m-30) REVERT: ppp 12 ASP cc_start: 0.9434 (m-30) cc_final: 0.9149 (m-30) REVERT: MMM 19 THR cc_start: 0.9705 (m) cc_final: 0.9458 (p) REVERT: MMM 24 TYR cc_start: 0.9541 (m-10) cc_final: 0.9232 (m-10) REVERT: MMM 29 VAL cc_start: 0.9657 (t) cc_final: 0.9364 (m) REVERT: MMM 39 ILE cc_start: 0.9591 (mt) cc_final: 0.9164 (mm) REVERT: MMM 43 LYS cc_start: 0.9542 (mtpt) cc_final: 0.9311 (mtpp) REVERT: MMM 44 LYS cc_start: 0.9511 (ttpt) cc_final: 0.9300 (ttpt) REVERT: MMM 48 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9130 (mtpp) REVERT: RRR 45 PHE cc_start: 0.9581 (m-80) cc_final: 0.9332 (m-80) REVERT: WWW 15 GLN cc_start: 0.9641 (tt0) cc_final: 0.9380 (tt0) REVERT: bbb 12 ASP cc_start: 0.9526 (m-30) cc_final: 0.9290 (p0) REVERT: bbb 15 GLN cc_start: 0.9408 (tt0) cc_final: 0.9160 (mt0) REVERT: bbb 29 VAL cc_start: 0.9808 (t) cc_final: 0.9602 (m) REVERT: bbb 40 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9001 (ttmt) REVERT: HHH 273 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: ggg 12 ASP cc_start: 0.9077 (m-30) cc_final: 0.8688 (m-30) REVERT: lll 8 LYS cc_start: 0.9456 (ttpt) cc_final: 0.9057 (ttmm) REVERT: lll 12 ASP cc_start: 0.9099 (m-30) cc_final: 0.8879 (m-30) REVERT: lll 48 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8858 (mmtm) REVERT: qqq 12 ASP cc_start: 0.9449 (m-30) cc_final: 0.9145 (m-30) REVERT: NNN 17 SER cc_start: 0.8503 (m) cc_final: 0.8002 (p) REVERT: NNN 19 THR cc_start: 0.9678 (m) cc_final: 0.9440 (p) REVERT: NNN 24 TYR cc_start: 0.9567 (m-10) cc_final: 0.9352 (m-10) REVERT: NNN 43 LYS cc_start: 0.9573 (mtpt) cc_final: 0.9347 (mtmt) REVERT: NNN 44 LYS cc_start: 0.9519 (ttpt) cc_final: 0.9240 (ttmt) REVERT: SSS 36 THR cc_start: 0.9632 (m) cc_final: 0.9397 (p) REVERT: SSS 39 ILE cc_start: 0.9625 (mt) cc_final: 0.9372 (pp) REVERT: SSS 40 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9197 (ttpp) REVERT: SSS 45 PHE cc_start: 0.9513 (m-80) cc_final: 0.9247 (m-80) REVERT: ccc 15 GLN cc_start: 0.9429 (tt0) cc_final: 0.9121 (mt0) REVERT: ccc 29 VAL cc_start: 0.9834 (t) cc_final: 0.9616 (m) REVERT: III 287 LYS cc_start: 0.9331 (mttt) cc_final: 0.9102 (mtmt) REVERT: mmm 8 LYS cc_start: 0.9404 (ttpt) cc_final: 0.8992 (ttmm) REVERT: mmm 12 ASP cc_start: 0.9082 (m-30) cc_final: 0.8838 (m-30) REVERT: mmm 21 MET cc_start: 0.9236 (mtp) cc_final: 0.8995 (tpp) REVERT: rrr 12 ASP cc_start: 0.9467 (m-30) cc_final: 0.9245 (m-30) REVERT: OOO 19 THR cc_start: 0.9720 (m) cc_final: 0.9508 (p) REVERT: OOO 24 TYR cc_start: 0.9534 (m-10) cc_final: 0.9027 (m-80) REVERT: OOO 39 ILE cc_start: 0.9564 (mt) cc_final: 0.9159 (mm) REVERT: OOO 48 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9154 (mtpp) REVERT: TTT 40 LYS cc_start: 0.9336 (ttmt) cc_final: 0.8951 (tttm) REVERT: TTT 41 LEU cc_start: 0.9764 (mt) cc_final: 0.9506 (mp) REVERT: TTT 42 PHE cc_start: 0.9371 (t80) cc_final: 0.9154 (t80) REVERT: TTT 45 PHE cc_start: 0.9522 (m-80) cc_final: 0.9217 (m-80) REVERT: ddd 15 GLN cc_start: 0.9421 (tt0) cc_final: 0.9133 (mt0) REVERT: ddd 20 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8988 (mp0) REVERT: ddd 21 MET cc_start: 0.9686 (mtp) cc_final: 0.9429 (mtp) REVERT: EEE 99 ASP cc_start: 0.8139 (m-30) cc_final: 0.7883 (m-30) REVERT: JJJ 263 MET cc_start: 0.8881 (tpt) cc_final: 0.8390 (tpt) REVERT: JJJ 267 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.8944 (m-40) REVERT: JJJ 273 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: JJJ 287 LYS cc_start: 0.9343 (mttt) cc_final: 0.9076 (mtmt) REVERT: iii 12 ASP cc_start: 0.9040 (m-30) cc_final: 0.8787 (m-30) REVERT: nnn 8 LYS cc_start: 0.9466 (ttpt) cc_final: 0.9261 (ttpp) REVERT: nnn 12 ASP cc_start: 0.9083 (m-30) cc_final: 0.8880 (m-30) REVERT: nnn 48 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8795 (mmtm) REVERT: sss 12 ASP cc_start: 0.9461 (m-30) cc_final: 0.9194 (m-30) outliers start: 92 outliers final: 11 residues processed: 765 average time/residue: 0.6028 time to fit residues: 519.5948 Evaluate side-chains 451 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 433 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ZZZ residue 11 PHE Chi-restraints excluded: chain FFF residue 345 LEU Chi-restraints excluded: chain aaa residue 11 PHE Chi-restraints excluded: chain GGG residue 267 ASN Chi-restraints excluded: chain GGG residue 345 LEU Chi-restraints excluded: chain GGG residue 376 LEU Chi-restraints excluded: chain MMM residue 48 LYS Chi-restraints excluded: chain bbb residue 11 PHE Chi-restraints excluded: chain HHH residue 273 GLU Chi-restraints excluded: chain HHH residue 345 LEU Chi-restraints excluded: chain ccc residue 11 PHE Chi-restraints excluded: chain III residue 345 LEU Chi-restraints excluded: chain OOO residue 48 LYS Chi-restraints excluded: chain ddd residue 11 PHE Chi-restraints excluded: chain JJJ residue 267 ASN Chi-restraints excluded: chain JJJ residue 273 GLU Chi-restraints excluded: chain JJJ residue 345 LEU Chi-restraints excluded: chain JJJ residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.039041 restraints weight = 66646.782| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.76 r_work: 0.2625 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20860 Z= 0.181 Angle : 0.630 6.911 28145 Z= 0.345 Chirality : 0.039 0.279 3320 Planarity : 0.005 0.047 3430 Dihedral : 5.325 40.923 2822 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.39 % Allowed : 22.21 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2630 helix: 0.51 (0.11), residues: 2200 sheet: None (None), residues: 0 loop : -2.12 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGGGG 402 TYR 0.012 0.001 TYRKKK 24 PHE 0.015 0.002 PHEeee 42 TRP 0.008 0.001 TRPmmm 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (20860) covalent geometry : angle 0.63015 / 0.34 (28145) hydrogen bonds : bond 0.08623 / 5.59 ( 1611) hydrogen bonds : angle 4.10438 / 2.87 ( 4773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 542 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: KKK 28 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9056 (pp-130) REVERT: PPP 28 MET cc_start: 0.7350 (pmm) cc_final: 0.7130 (mmm) REVERT: PPP 40 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9102 (tttt) REVERT: UUU 5 ASP cc_start: 0.8036 (t0) cc_final: 0.7714 (OUTLIER) REVERT: ZZZ 15 GLN cc_start: 0.9379 (tt0) cc_final: 0.9142 (mt0) REVERT: FFF 261 GLU cc_start: 0.8646 (pm20) cc_final: 0.8424 (pm20) REVERT: FFF 273 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7544 (mt-10) REVERT: FFF 395 SER cc_start: 0.9494 (m) cc_final: 0.9232 (p) REVERT: QQQ 28 MET cc_start: 0.7521 (pmm) cc_final: 0.7264 (mmt) REVERT: QQQ 48 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9162 (mtpp) REVERT: VVV 5 ASP cc_start: 0.7904 (t0) cc_final: 0.7695 (t0) REVERT: aaa 29 VAL cc_start: 0.9766 (t) cc_final: 0.9552 (p) REVERT: GGG 261 GLU cc_start: 0.8721 (pm20) cc_final: 0.8506 (pm20) REVERT: GGG 353 GLU cc_start: 0.7466 (pp20) cc_final: 0.7128 (pp20) REVERT: kkk 5 ASP cc_start: 0.7505 (t0) cc_final: 0.7084 (t0) REVERT: ppp 8 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8789 (mmmm) REVERT: ppp 29 VAL cc_start: 0.9696 (t) cc_final: 0.9425 (p) REVERT: MMM 24 TYR cc_start: 0.9325 (m-10) cc_final: 0.9044 (m-10) REVERT: WWW 5 ASP cc_start: 0.7998 (t0) cc_final: 0.7664 (t0) REVERT: WWW 40 LYS cc_start: 0.9574 (ttmm) cc_final: 0.9203 (ttpt) REVERT: HHH 261 GLU cc_start: 0.8683 (pm20) cc_final: 0.8480 (pm20) REVERT: HHH 262 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9006 (ttpp) REVERT: HHH 273 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7570 (mt-10) REVERT: ggg 44 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8908 (tmmm) REVERT: SSS 44 LYS cc_start: 0.9387 (ttmt) cc_final: 0.9155 (ttmt) REVERT: SSS 48 LYS cc_start: 0.9417 (mtpp) cc_final: 0.9169 (mtpp) REVERT: XXX 5 ASP cc_start: 0.8027 (t0) cc_final: 0.7616 (OUTLIER) REVERT: XXX 40 LYS cc_start: 0.9588 (ttmm) cc_final: 0.9144 (ttpt) REVERT: ccc 22 ILE cc_start: 0.9119 (pp) cc_final: 0.8915 (pp) REVERT: ccc 41 LEU cc_start: 0.9808 (mt) cc_final: 0.9545 (mm) REVERT: III 261 GLU cc_start: 0.8710 (pm20) cc_final: 0.8479 (pm20) REVERT: III 273 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7979 (mt-10) REVERT: III 353 GLU cc_start: 0.7524 (pp20) cc_final: 0.7297 (pp20) REVERT: III 355 ARG cc_start: 0.8784 (mtm-85) cc_final: 0.8578 (mtm-85) REVERT: mmm 8 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8959 (ptmm) REVERT: mmm 22 ILE cc_start: 0.9482 (mt) cc_final: 0.9254 (mp) REVERT: mmm 40 LYS cc_start: 0.9348 (ttmm) cc_final: 0.8807 (ttpt) REVERT: rrr 29 VAL cc_start: 0.9730 (t) cc_final: 0.9525 (p) REVERT: TTT 48 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9066 (mtpp) REVERT: ddd 20 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9184 (mp0) REVERT: JJJ 271 MET cc_start: 0.9346 (mtp) cc_final: 0.9079 (mtm) REVERT: JJJ 273 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7822 (mt-10) REVERT: nnn 22 ILE cc_start: 0.9478 (mt) cc_final: 0.9232 (mp) REVERT: sss 8 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8837 (mmmm) REVERT: sss 29 VAL cc_start: 0.9719 (t) cc_final: 0.9463 (p) outliers start: 72 outliers final: 12 residues processed: 581 average time/residue: 0.5958 time to fit residues: 391.1600 Evaluate side-chains 398 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 385 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain PPP residue 37 ILE Chi-restraints excluded: chain FFF residue 345 LEU Chi-restraints excluded: chain GGG residue 345 LEU Chi-restraints excluded: chain ppp residue 8 LYS Chi-restraints excluded: chain HHH residue 262 LYS Chi-restraints excluded: chain HHH residue 345 LEU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 39 ILE Chi-restraints excluded: chain III residue 262 LYS Chi-restraints excluded: chain III residue 345 LEU Chi-restraints excluded: chain YYY residue 5 ASP Chi-restraints excluded: chain JJJ residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.036899 restraints weight = 67099.129| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.76 r_work: 0.2542 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20860 Z= 0.167 Angle : 0.581 7.405 28145 Z= 0.318 Chirality : 0.038 0.217 3320 Planarity : 0.004 0.048 3430 Dihedral : 4.312 40.307 2790 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.29 % Allowed : 25.13 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2630 helix: 1.55 (0.11), residues: 2195 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBBB 12 TYR 0.012 0.001 TYRKKK 24 PHE 0.016 0.002 PHECCC 43 TRP 0.006 0.001 TRPDDD 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (20860) covalent geometry : angle 0.58097 / 0.32 (28145) hydrogen bonds : bond 0.07903 / 5.13 ( 1611) hydrogen bonds : angle 3.77124 / 2.65 ( 4773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 441 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: KKK 24 TYR cc_start: 0.9330 (m-10) cc_final: 0.9107 (m-10) REVERT: KKK 28 MET cc_start: 0.9560 (ttm) cc_final: 0.8956 (pp-130) REVERT: PPP 40 LYS cc_start: 0.9345 (ttmt) cc_final: 0.9108 (tttt) REVERT: UUU 40 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9290 (ttpt) REVERT: ZZZ 41 LEU cc_start: 0.9726 (mt) cc_final: 0.9482 (mm) REVERT: FFF 261 GLU cc_start: 0.8681 (pm20) cc_final: 0.8478 (pm20) REVERT: FFF 273 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7634 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7149 (pp20) cc_final: 0.6911 (pp20) REVERT: FFF 395 SER cc_start: 0.9396 (m) cc_final: 0.9065 (p) REVERT: ooo 29 VAL cc_start: 0.9742 (t) cc_final: 0.9525 (p) REVERT: LLL 20 GLU cc_start: 0.9545 (pt0) cc_final: 0.9304 (pm20) REVERT: QQQ 28 MET cc_start: 0.7661 (pmm) cc_final: 0.7350 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.7879 (p) REVERT: QQQ 48 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9169 (mtpp) REVERT: aaa 40 LYS cc_start: 0.9541 (ttmt) cc_final: 0.9328 (tttt) REVERT: GGG 261 GLU cc_start: 0.8732 (pm20) cc_final: 0.8509 (pm20) REVERT: GGG 273 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8154 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7384 (pp20) cc_final: 0.7076 (pp20) REVERT: fff 20 GLU cc_start: 0.8550 (mp0) cc_final: 0.8162 (mp0) REVERT: MMM 24 TYR cc_start: 0.9440 (m-10) cc_final: 0.9194 (m-10) REVERT: WWW 40 LYS cc_start: 0.9544 (ttmm) cc_final: 0.9294 (ttpt) REVERT: bbb 11 PHE cc_start: 0.8773 (m-80) cc_final: 0.8421 (m-80) REVERT: bbb 12 ASP cc_start: 0.9531 (m-30) cc_final: 0.9278 (p0) REVERT: bbb 15 GLN cc_start: 0.9179 (mt0) cc_final: 0.8767 (mm110) REVERT: HHH 273 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7518 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7185 (pp20) cc_final: 0.6942 (pp20) REVERT: ggg 20 GLU cc_start: 0.8617 (mp0) cc_final: 0.8327 (mp0) REVERT: ggg 44 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8958 (tmmm) REVERT: lll 40 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8758 (ttpt) REVERT: qqq 20 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: NNN 21 MET cc_start: 0.7991 (ttt) cc_final: 0.7732 (mmm) REVERT: XXX 40 LYS cc_start: 0.9546 (ttmm) cc_final: 0.9155 (ttpt) REVERT: ccc 22 ILE cc_start: 0.9158 (pp) cc_final: 0.8957 (pp) REVERT: ccc 41 LEU cc_start: 0.9714 (mt) cc_final: 0.9509 (mm) REVERT: III 261 GLU cc_start: 0.8703 (pm20) cc_final: 0.8450 (pm20) REVERT: III 273 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7967 (mt-10) REVERT: III 353 GLU cc_start: 0.7728 (pp20) cc_final: 0.7465 (pp20) REVERT: hhh 20 GLU cc_start: 0.8701 (mp0) cc_final: 0.8421 (mp0) REVERT: hhh 47 SER cc_start: 0.8071 (t) cc_final: 0.7733 (p) REVERT: mmm 5 ASP cc_start: 0.7733 (t0) cc_final: 0.7419 (t0) REVERT: mmm 29 VAL cc_start: 0.9372 (t) cc_final: 0.9168 (p) REVERT: TTT 48 LYS cc_start: 0.9228 (mtpp) cc_final: 0.8987 (mtpp) REVERT: YYY 12 ASP cc_start: 0.9613 (m-30) cc_final: 0.9268 (p0) REVERT: YYY 15 GLN cc_start: 0.9492 (mt0) cc_final: 0.9133 (mt0) REVERT: ddd 21 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9367 (mtp) REVERT: ddd 40 LYS cc_start: 0.9494 (ttmt) cc_final: 0.9288 (ttmt) REVERT: ddd 41 LEU cc_start: 0.9747 (mt) cc_final: 0.9473 (mm) REVERT: JJJ 261 GLU cc_start: 0.8601 (pm20) cc_final: 0.8382 (pm20) REVERT: JJJ 271 MET cc_start: 0.9241 (mtp) cc_final: 0.8960 (mtm) REVERT: JJJ 273 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7881 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7598 (pp20) cc_final: 0.7315 (pp20) REVERT: nnn 20 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8899 (mt-10) REVERT: sss 5 ASP cc_start: 0.8104 (t0) cc_final: 0.7804 (t0) outliers start: 70 outliers final: 26 residues processed: 488 average time/residue: 0.6185 time to fit residues: 341.3176 Evaluate side-chains 416 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 387 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PPP residue 29 VAL Chi-restraints excluded: chain UUU residue 47 SER Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 111 ASP Chi-restraints excluded: chain FFF residue 316 THR Chi-restraints excluded: chain ooo residue 47 SER Chi-restraints excluded: chain QQQ residue 29 VAL Chi-restraints excluded: chain VVV residue 47 SER Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 53 ILE Chi-restraints excluded: chain BBB residue 60 ASP Chi-restraints excluded: chain GGG residue 316 THR Chi-restraints excluded: chain GGG residue 345 LEU Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 46 THR Chi-restraints excluded: chain ppp residue 47 SER Chi-restraints excluded: chain RRR residue 29 VAL Chi-restraints excluded: chain WWW residue 28 MET Chi-restraints excluded: chain CCC residue 53 ILE Chi-restraints excluded: chain CCC residue 95 ILE Chi-restraints excluded: chain HHH residue 316 THR Chi-restraints excluded: chain ggg residue 47 SER Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain YYY residue 5 ASP Chi-restraints excluded: chain ddd residue 21 MET Chi-restraints excluded: chain JJJ residue 316 THR Chi-restraints excluded: chain JJJ residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 237 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 224 optimal weight: 0.0170 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037185 restraints weight = 67752.417| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.82 r_work: 0.2562 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20860 Z= 0.157 Angle : 0.574 6.204 28145 Z= 0.311 Chirality : 0.038 0.183 3320 Planarity : 0.004 0.034 3430 Dihedral : 3.809 38.760 2784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.54 % Allowed : 27.67 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 2630 helix: 1.93 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBBB 12 TYR 0.011 0.001 TYRbbb 24 PHE 0.013 0.001 PHECCC 43 TRP 0.010 0.001 TRPAAA 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (20860) covalent geometry : angle 0.57406 / 0.31 (28145) hydrogen bonds : bond 0.07138 / 4.64 ( 1611) hydrogen bonds : angle 3.64060 / 2.57 ( 4773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 428 time to evaluate : 0.909 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: KKK 21 MET cc_start: 0.8017 (mtp) cc_final: 0.7772 (mtm) REVERT: KKK 28 MET cc_start: 0.9518 (ttm) cc_final: 0.8981 (pp-130) REVERT: PPP 40 LYS cc_start: 0.9294 (ttmt) cc_final: 0.9056 (tttt) REVERT: ZZZ 41 LEU cc_start: 0.9701 (mt) cc_final: 0.9483 (mm) REVERT: AAA 111 ASP cc_start: 0.8595 (t0) cc_final: 0.8320 (t0) REVERT: FFF 261 GLU cc_start: 0.8676 (pm20) cc_final: 0.8474 (pm20) REVERT: FFF 273 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7745 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7345 (pp20) cc_final: 0.7057 (pp20) REVERT: FFF 395 SER cc_start: 0.9374 (m) cc_final: 0.9054 (p) REVERT: eee 20 GLU cc_start: 0.8629 (mp0) cc_final: 0.8401 (mp0) REVERT: ooo 20 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8693 (mp0) REVERT: ooo 29 VAL cc_start: 0.9756 (t) cc_final: 0.9533 (p) REVERT: LLL 20 GLU cc_start: 0.9538 (pt0) cc_final: 0.9281 (pm20) REVERT: QQQ 28 MET cc_start: 0.8010 (pmm) cc_final: 0.7736 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8341 (m) cc_final: 0.7962 (p) REVERT: VVV 15 GLN cc_start: 0.9517 (tt0) cc_final: 0.9230 (mt0) REVERT: GGG 261 GLU cc_start: 0.8730 (pm20) cc_final: 0.8524 (pm20) REVERT: GGG 273 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8232 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7529 (pp20) cc_final: 0.7179 (pp20) REVERT: fff 20 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: kkk 40 LYS cc_start: 0.9298 (ttpt) cc_final: 0.9077 (tttt) REVERT: RRR 29 VAL cc_start: 0.8133 (m) cc_final: 0.7926 (p) REVERT: bbb 11 PHE cc_start: 0.8656 (m-80) cc_final: 0.8256 (m-80) REVERT: bbb 15 GLN cc_start: 0.9263 (mt0) cc_final: 0.8911 (mm110) REVERT: HHH 273 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7587 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7332 (pp20) cc_final: 0.7055 (pp20) REVERT: ggg 20 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: lll 40 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8783 (ttpt) REVERT: NNN 21 MET cc_start: 0.7679 (ttt) cc_final: 0.7463 (mmm) REVERT: SSS 48 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8837 (mtpp) REVERT: ccc 15 GLN cc_start: 0.9279 (mt0) cc_final: 0.8775 (mm110) REVERT: ccc 41 LEU cc_start: 0.9699 (mt) cc_final: 0.9472 (mm) REVERT: III 261 GLU cc_start: 0.8703 (pm20) cc_final: 0.8453 (pm20) REVERT: III 273 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8099 (mt-10) REVERT: III 353 GLU cc_start: 0.7837 (pp20) cc_final: 0.7539 (pp20) REVERT: hhh 20 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: mmm 20 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9000 (mt-10) REVERT: mmm 29 VAL cc_start: 0.9393 (t) cc_final: 0.9165 (p) REVERT: rrr 5 ASP cc_start: 0.8461 (t0) cc_final: 0.8120 (t0) REVERT: OOO 21 MET cc_start: 0.7874 (mtp) cc_final: 0.7666 (mmm) REVERT: YYY 5 ASP cc_start: 0.7752 (t0) cc_final: 0.7163 (t0) REVERT: YYY 8 LYS cc_start: 0.9203 (ptmm) cc_final: 0.8953 (mtmm) REVERT: YYY 15 GLN cc_start: 0.9492 (mt0) cc_final: 0.9176 (mt0) REVERT: ddd 15 GLN cc_start: 0.9262 (mt0) cc_final: 0.8907 (mm110) REVERT: ddd 21 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.9350 (mtp) REVERT: ddd 40 LYS cc_start: 0.9498 (ttmt) cc_final: 0.9290 (ttmt) REVERT: ddd 41 LEU cc_start: 0.9718 (mt) cc_final: 0.9450 (mm) REVERT: JJJ 261 GLU cc_start: 0.8689 (pm20) cc_final: 0.8461 (pm20) REVERT: JJJ 271 MET cc_start: 0.9191 (mtp) cc_final: 0.8929 (mtm) REVERT: JJJ 273 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7964 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7689 (pp20) cc_final: 0.7354 (pp20) REVERT: iii 20 GLU cc_start: 0.8761 (mp0) cc_final: 0.8518 (mp0) REVERT: nnn 40 LYS cc_start: 0.9294 (ttmt) cc_final: 0.8799 (tttt) outliers start: 54 outliers final: 26 residues processed: 465 average time/residue: 0.6163 time to fit residues: 323.2735 Evaluate side-chains 412 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PPP residue 29 VAL Chi-restraints excluded: chain UUU residue 5 ASP Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain FFF residue 316 THR Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain VVV residue 5 ASP Chi-restraints excluded: chain aaa residue 32 ILE Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain GGG residue 316 THR Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 5 ASP Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 53 ILE Chi-restraints excluded: chain HHH residue 316 THR Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain lll residue 21 MET Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain SSS residue 37 ILE Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain III residue 262 LYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain ddd residue 21 MET Chi-restraints excluded: chain EEE residue 53 ILE Chi-restraints excluded: chain JJJ residue 316 THR Chi-restraints excluded: chain JJJ residue 345 LEU Chi-restraints excluded: chain JJJ residue 371 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 179 optimal weight: 0.0670 chunk 194 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 19 optimal weight: 0.0070 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.040121 restraints weight = 66423.218| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.74 r_work: 0.2636 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20860 Z= 0.138 Angle : 0.560 6.258 28145 Z= 0.300 Chirality : 0.037 0.188 3320 Planarity : 0.003 0.034 3430 Dihedral : 3.605 33.806 2782 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.73 % Allowed : 27.58 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.16), residues: 2630 helix: 2.21 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -0.90 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGGG 342 TYR 0.014 0.001 TYRKKK 24 PHE 0.009 0.001 PHEDDD 16 TRP 0.005 0.000 TRPUUU 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (20860) covalent geometry : angle 0.55999 / 0.30 (28145) hydrogen bonds : bond 0.06201 / 4.04 ( 1611) hydrogen bonds : angle 3.44275 / 2.44 ( 4773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 443 time to evaluate : 0.854 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: KKK 21 MET cc_start: 0.7922 (mtp) cc_final: 0.7686 (mtm) REVERT: KKK 28 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.8892 (pp-130) REVERT: PPP 40 LYS cc_start: 0.9226 (ttmt) cc_final: 0.9020 (tttt) REVERT: ZZZ 11 PHE cc_start: 0.8797 (m-80) cc_final: 0.8216 (m-80) REVERT: ZZZ 15 GLN cc_start: 0.9299 (mm-40) cc_final: 0.9007 (mm110) REVERT: AAA 111 ASP cc_start: 0.8486 (t0) cc_final: 0.8135 (t0) REVERT: FFF 261 GLU cc_start: 0.8643 (pm20) cc_final: 0.8440 (pm20) REVERT: FFF 273 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7897 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7327 (pp20) cc_final: 0.6999 (pp20) REVERT: FFF 395 SER cc_start: 0.9366 (m) cc_final: 0.8983 (p) REVERT: eee 20 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: jjj 20 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8332 (mt-10) REVERT: jjj 47 SER cc_start: 0.8638 (m) cc_final: 0.8435 (p) REVERT: ooo 5 ASP cc_start: 0.8074 (t0) cc_final: 0.7743 (t0) REVERT: ooo 29 VAL cc_start: 0.9748 (t) cc_final: 0.9527 (p) REVERT: LLL 20 GLU cc_start: 0.9529 (pt0) cc_final: 0.9265 (pm20) REVERT: QQQ 28 MET cc_start: 0.8050 (pmm) cc_final: 0.7790 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7813 (p) REVERT: VVV 5 ASP cc_start: 0.7672 (t0) cc_final: 0.7192 (t0) REVERT: aaa 11 PHE cc_start: 0.8625 (m-80) cc_final: 0.8293 (m-10) REVERT: aaa 15 GLN cc_start: 0.9207 (mt0) cc_final: 0.8981 (mm110) REVERT: GGG 261 GLU cc_start: 0.8675 (pm20) cc_final: 0.8461 (pm20) REVERT: GGG 262 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9044 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8273 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7474 (pp20) cc_final: 0.7038 (pp20) REVERT: fff 20 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: kkk 47 SER cc_start: 0.8616 (m) cc_final: 0.8396 (p) REVERT: kkk 50 SER cc_start: 0.7820 (t) cc_final: 0.7599 (m) REVERT: bbb 11 PHE cc_start: 0.8706 (m-80) cc_final: 0.8300 (m-80) REVERT: bbb 15 GLN cc_start: 0.9256 (mt0) cc_final: 0.8935 (mm110) REVERT: HHH 262 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8857 (ttpp) REVERT: HHH 273 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7464 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7238 (pp20) cc_final: 0.6929 (pp20) REVERT: ggg 20 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: lll 40 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8735 (tttt) REVERT: lll 47 SER cc_start: 0.8626 (m) cc_final: 0.8386 (p) REVERT: qqq 21 MET cc_start: 0.9374 (mtp) cc_final: 0.9041 (mmm) REVERT: NNN 28 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6767 (pp-130) REVERT: XXX 5 ASP cc_start: 0.7375 (t0) cc_final: 0.6133 (OUTLIER) REVERT: ccc 15 GLN cc_start: 0.9244 (mt0) cc_final: 0.8904 (mm110) REVERT: DDD 111 ASP cc_start: 0.8444 (t70) cc_final: 0.8215 (t0) REVERT: III 261 GLU cc_start: 0.8690 (pm20) cc_final: 0.8425 (pm20) REVERT: III 273 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8128 (mt-10) REVERT: III 353 GLU cc_start: 0.7862 (pp20) cc_final: 0.7507 (pp20) REVERT: hhh 20 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: mmm 29 VAL cc_start: 0.9365 (t) cc_final: 0.9138 (p) REVERT: OOO 28 MET cc_start: 0.9571 (ttp) cc_final: 0.9206 (pp-130) REVERT: TTT 48 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8897 (mtpt) REVERT: YYY 5 ASP cc_start: 0.7642 (t0) cc_final: 0.6818 (OUTLIER) REVERT: YYY 15 GLN cc_start: 0.9479 (mt0) cc_final: 0.9175 (mt0) REVERT: ddd 15 GLN cc_start: 0.9249 (mt0) cc_final: 0.8832 (mm110) REVERT: ddd 21 MET cc_start: 0.9568 (mtm) cc_final: 0.9328 (mtp) REVERT: ddd 41 LEU cc_start: 0.9672 (mt) cc_final: 0.9376 (mm) REVERT: JJJ 261 GLU cc_start: 0.8662 (pm20) cc_final: 0.8461 (pm20) REVERT: JJJ 271 MET cc_start: 0.9175 (mtp) cc_final: 0.8967 (mtm) REVERT: JJJ 273 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7827 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7652 (pp20) cc_final: 0.7274 (pp20) REVERT: iii 20 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: iii 44 LYS cc_start: 0.8925 (tppt) cc_final: 0.8703 (tttm) REVERT: nnn 40 LYS cc_start: 0.9206 (ttmt) cc_final: 0.8740 (tttt) REVERT: nnn 50 SER cc_start: 0.7565 (t) cc_final: 0.7158 (m) outliers start: 58 outliers final: 19 residues processed: 476 average time/residue: 0.5935 time to fit residues: 319.5666 Evaluate side-chains 406 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 379 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain QQQ residue 29 VAL Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain aaa residue 32 ILE Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain HHH residue 262 LYS Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain NNN residue 28 MET Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain iii residue 20 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 237 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.037658 restraints weight = 67477.678| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.84 r_work: 0.2576 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20860 Z= 0.150 Angle : 0.588 7.376 28145 Z= 0.316 Chirality : 0.039 0.219 3320 Planarity : 0.003 0.032 3430 Dihedral : 3.449 21.628 2780 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.01 % Allowed : 28.00 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.16), residues: 2630 helix: 2.30 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -0.72 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGGG 355 TYR 0.011 0.001 TYRKKK 24 PHE 0.014 0.001 PHECCC 43 TRP 0.004 0.001 TRPVVV 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (20860) covalent geometry : angle 0.58755 / 0.32 (28145) hydrogen bonds : bond 0.06601 / 4.29 ( 1611) hydrogen bonds : angle 3.52172 / 2.49 ( 4773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 396 time to evaluate : 0.654 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: KKK 20 GLU cc_start: 0.8925 (pp20) cc_final: 0.8690 (pp20) REVERT: KKK 21 MET cc_start: 0.7860 (mtp) cc_final: 0.7588 (mmm) REVERT: KKK 28 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.8895 (pp-130) REVERT: ZZZ 11 PHE cc_start: 0.8807 (m-80) cc_final: 0.8236 (m-80) REVERT: ZZZ 15 GLN cc_start: 0.9288 (mm-40) cc_final: 0.9061 (mm110) REVERT: ZZZ 40 LYS cc_start: 0.9345 (tttp) cc_final: 0.8991 (tttp) REVERT: ZZZ 41 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9389 (mm) REVERT: FFF 273 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7812 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7598 (pp20) cc_final: 0.7191 (pp20) REVERT: FFF 395 SER cc_start: 0.9348 (m) cc_final: 0.8982 (p) REVERT: eee 20 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: jjj 20 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8624 (mt-10) REVERT: jjj 47 SER cc_start: 0.8726 (m) cc_final: 0.8523 (p) REVERT: jjj 50 SER cc_start: 0.7576 (m) cc_final: 0.7340 (t) REVERT: ooo 21 MET cc_start: 0.9399 (mmt) cc_final: 0.9192 (mtp) REVERT: ooo 29 VAL cc_start: 0.9750 (t) cc_final: 0.9521 (p) REVERT: LLL 20 GLU cc_start: 0.9591 (pt0) cc_final: 0.9318 (pm20) REVERT: QQQ 28 MET cc_start: 0.8105 (pmm) cc_final: 0.7813 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7906 (p) REVERT: aaa 11 PHE cc_start: 0.8643 (m-80) cc_final: 0.8275 (m-80) REVERT: aaa 15 GLN cc_start: 0.9206 (mt0) cc_final: 0.8979 (mm110) REVERT: GGG 261 GLU cc_start: 0.8764 (pm20) cc_final: 0.8556 (pm20) REVERT: GGG 262 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9027 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8285 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7599 (pp20) cc_final: 0.7163 (pp20) REVERT: fff 20 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: kkk 47 SER cc_start: 0.8737 (m) cc_final: 0.8505 (p) REVERT: kkk 50 SER cc_start: 0.8016 (t) cc_final: 0.7751 (m) REVERT: bbb 11 PHE cc_start: 0.8743 (m-80) cc_final: 0.8284 (m-80) REVERT: bbb 15 GLN cc_start: 0.9280 (mt0) cc_final: 0.8987 (mm110) REVERT: HHH 262 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8694 (ttpp) REVERT: HHH 273 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7451 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7402 (pp20) cc_final: 0.7066 (pp20) REVERT: ggg 20 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: lll 40 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8785 (ttpt) REVERT: NNN 28 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6788 (pp-130) REVERT: ccc 15 GLN cc_start: 0.9253 (mt0) cc_final: 0.8921 (mm110) REVERT: ccc 40 LYS cc_start: 0.9416 (tttp) cc_final: 0.9211 (tttt) REVERT: DDD 111 ASP cc_start: 0.8594 (t70) cc_final: 0.8385 (t70) REVERT: III 261 GLU cc_start: 0.8776 (pm20) cc_final: 0.8534 (pm20) REVERT: III 273 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8093 (mt-10) REVERT: III 353 GLU cc_start: 0.7931 (pp20) cc_final: 0.7537 (pp20) REVERT: hhh 20 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: mmm 29 VAL cc_start: 0.9372 (t) cc_final: 0.9133 (p) REVERT: OOO 28 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.9121 (pp-130) REVERT: TTT 48 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8895 (mtpt) REVERT: ddd 15 GLN cc_start: 0.9280 (mt0) cc_final: 0.8904 (mm110) REVERT: ddd 21 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9196 (mtp) REVERT: ddd 40 LYS cc_start: 0.9533 (tttp) cc_final: 0.9303 (tttt) REVERT: JJJ 261 GLU cc_start: 0.8694 (pm20) cc_final: 0.8484 (pm20) REVERT: JJJ 271 MET cc_start: 0.9133 (mtp) cc_final: 0.8867 (mtm) REVERT: JJJ 273 GLU cc_start: 0.8760 (mt-10) cc_final: 0.7934 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7818 (pp20) cc_final: 0.7420 (pp20) REVERT: iii 20 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: iii 44 LYS cc_start: 0.9015 (tppt) cc_final: 0.8731 (tttm) REVERT: nnn 40 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8753 (tttt) REVERT: nnn 50 SER cc_start: 0.7838 (t) cc_final: 0.7413 (m) outliers start: 64 outliers final: 26 residues processed: 435 average time/residue: 0.6315 time to fit residues: 308.9032 Evaluate side-chains 412 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain ZZZ residue 41 LEU Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 47 ILE Chi-restraints excluded: chain AAA residue 55 VAL Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain QQQ residue 29 VAL Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain VVV residue 20 GLU Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 47 ILE Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain fff residue 48 LYS Chi-restraints excluded: chain RRR residue 29 VAL Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 53 ILE Chi-restraints excluded: chain HHH residue 262 LYS Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 5 ASP Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain NNN residue 28 MET Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain DDD residue 47 ILE Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain OOO residue 28 MET Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain ddd residue 21 MET Chi-restraints excluded: chain JJJ residue 316 THR Chi-restraints excluded: chain iii residue 20 GLU Chi-restraints excluded: chain nnn residue 40 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 223 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 105 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.039206 restraints weight = 67470.931| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.84 r_work: 0.2626 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20860 Z= 0.138 Angle : 0.591 8.252 28145 Z= 0.315 Chirality : 0.039 0.213 3320 Planarity : 0.003 0.036 3430 Dihedral : 3.387 17.917 2780 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.45 % Allowed : 29.04 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.16), residues: 2630 helix: 2.41 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -0.49 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGGG 355 TYR 0.018 0.001 TYRKKK 24 PHE 0.010 0.001 PHEBBB 16 TRP 0.005 0.000 TRPVVV 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (20860) covalent geometry : angle 0.59073 / 0.32 (28145) hydrogen bonds : bond 0.06032 / 3.93 ( 1611) hydrogen bonds : angle 3.43569 / 2.44 ( 4773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 413 time to evaluate : 0.870 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: KKK 20 GLU cc_start: 0.8908 (pp20) cc_final: 0.8651 (pp20) REVERT: KKK 21 MET cc_start: 0.7768 (mtp) cc_final: 0.7518 (mmm) REVERT: KKK 28 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.8868 (pp-130) REVERT: UUU 5 ASP cc_start: 0.7038 (t0) cc_final: 0.6176 (OUTLIER) REVERT: UUU 8 LYS cc_start: 0.9259 (ptmm) cc_final: 0.8945 (pttt) REVERT: UUU 12 ASP cc_start: 0.9529 (m-30) cc_final: 0.9094 (p0) REVERT: ZZZ 11 PHE cc_start: 0.8832 (m-80) cc_final: 0.8253 (m-80) REVERT: ZZZ 15 GLN cc_start: 0.9322 (mm-40) cc_final: 0.9115 (mm110) REVERT: ZZZ 41 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9395 (mm) REVERT: FFF 273 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7914 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7739 (pp20) cc_final: 0.7253 (pp20) REVERT: FFF 395 SER cc_start: 0.9335 (m) cc_final: 0.8920 (p) REVERT: eee 20 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: jjj 20 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8340 (mt-10) REVERT: jjj 47 SER cc_start: 0.8625 (m) cc_final: 0.8421 (p) REVERT: jjj 50 SER cc_start: 0.7554 (m) cc_final: 0.7312 (t) REVERT: ooo 21 MET cc_start: 0.9411 (mmt) cc_final: 0.9193 (mtp) REVERT: ooo 29 VAL cc_start: 0.9744 (t) cc_final: 0.9518 (p) REVERT: LLL 20 GLU cc_start: 0.9608 (pt0) cc_final: 0.9365 (pm20) REVERT: QQQ 28 MET cc_start: 0.8368 (pmm) cc_final: 0.8065 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7942 (p) REVERT: aaa 11 PHE cc_start: 0.8632 (m-80) cc_final: 0.8225 (m-80) REVERT: aaa 15 GLN cc_start: 0.9205 (mt0) cc_final: 0.8982 (mm110) REVERT: GGG 261 GLU cc_start: 0.8678 (pm20) cc_final: 0.8450 (pm20) REVERT: GGG 262 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9050 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8277 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7655 (pp20) cc_final: 0.7186 (pp20) REVERT: fff 20 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: fff 44 LYS cc_start: 0.8817 (tmmm) cc_final: 0.8605 (tmtt) REVERT: kkk 47 SER cc_start: 0.8659 (m) cc_final: 0.8431 (p) REVERT: WWW 5 ASP cc_start: 0.7176 (t0) cc_final: 0.6188 (t0) REVERT: bbb 11 PHE cc_start: 0.8777 (m-80) cc_final: 0.8270 (m-80) REVERT: bbb 15 GLN cc_start: 0.9306 (mt0) cc_final: 0.9040 (mm110) REVERT: HHH 273 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7494 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7488 (pp20) cc_final: 0.7137 (pp20) REVERT: ggg 20 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: lll 40 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8799 (tttt) REVERT: qqq 20 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8852 (mp0) REVERT: qqq 21 MET cc_start: 0.9361 (mtp) cc_final: 0.9119 (mmm) REVERT: NNN 24 TYR cc_start: 0.9394 (m-10) cc_final: 0.9163 (m-10) REVERT: XXX 5 ASP cc_start: 0.6941 (t0) cc_final: 0.6654 (t0) REVERT: XXX 12 ASP cc_start: 0.9501 (m-30) cc_final: 0.9038 (p0) REVERT: ccc 15 GLN cc_start: 0.9259 (mt0) cc_final: 0.8947 (mm110) REVERT: III 261 GLU cc_start: 0.8781 (pm20) cc_final: 0.8523 (pm20) REVERT: III 273 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8180 (mt-10) REVERT: III 353 GLU cc_start: 0.7982 (pp20) cc_final: 0.7554 (pp20) REVERT: III 355 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8561 (mtm-85) REVERT: hhh 20 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: mmm 29 VAL cc_start: 0.9401 (t) cc_final: 0.9146 (p) REVERT: OOO 28 MET cc_start: 0.9521 (ttp) cc_final: 0.9099 (pp-130) REVERT: YYY 32 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (mp) REVERT: ddd 15 GLN cc_start: 0.9271 (mt0) cc_final: 0.8950 (mm110) REVERT: ddd 40 LYS cc_start: 0.9551 (tttp) cc_final: 0.9317 (tttt) REVERT: JJJ 261 GLU cc_start: 0.8691 (pm20) cc_final: 0.8479 (pm20) REVERT: JJJ 273 GLU cc_start: 0.8743 (mt-10) cc_final: 0.7856 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7865 (pp20) cc_final: 0.7454 (pp20) REVERT: iii 20 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: iii 44 LYS cc_start: 0.8980 (tppt) cc_final: 0.8779 (tmmm) REVERT: nnn 40 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8913 (tttt) REVERT: nnn 50 SER cc_start: 0.7698 (t) cc_final: 0.7341 (m) outliers start: 52 outliers final: 26 residues processed: 443 average time/residue: 0.6118 time to fit residues: 305.2329 Evaluate side-chains 408 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 371 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain UUU residue 20 GLU Chi-restraints excluded: chain ZZZ residue 41 LEU Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 47 ILE Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain QQQ residue 29 VAL Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain VVV residue 20 GLU Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 47 ILE Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 20 GLU Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 47 ILE Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain XXX residue 21 MET Chi-restraints excluded: chain ccc residue 21 MET Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain DDD residue 47 ILE Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain YYY residue 32 ILE Chi-restraints excluded: chain EEE residue 47 ILE Chi-restraints excluded: chain iii residue 20 GLU Chi-restraints excluded: chain nnn residue 40 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 29 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 chunk 170 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038666 restraints weight = 67434.986| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.83 r_work: 0.2613 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20860 Z= 0.143 Angle : 0.608 9.687 28145 Z= 0.325 Chirality : 0.039 0.236 3320 Planarity : 0.003 0.031 3430 Dihedral : 3.336 16.591 2780 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.02 % Allowed : 30.49 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.16), residues: 2630 helix: 2.45 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -0.30 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGGG 355 TYR 0.013 0.001 TYRKKK 24 PHE 0.013 0.001 PHEAAA 43 TRP 0.005 0.000 TRPNNN 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (20860) covalent geometry : angle 0.60823 / 0.33 (28145) hydrogen bonds : bond 0.06148 / 4.00 ( 1611) hydrogen bonds : angle 3.46657 / 2.46 ( 4773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 403 time to evaluate : 0.827 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: KKK 20 GLU cc_start: 0.8913 (pp20) cc_final: 0.8681 (pp20) REVERT: KKK 21 MET cc_start: 0.7779 (mtp) cc_final: 0.7540 (mmm) REVERT: KKK 28 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8825 (pp-130) REVERT: KKK 40 LYS cc_start: 0.9474 (tttp) cc_final: 0.9262 (ttpt) REVERT: UUU 5 ASP cc_start: 0.6993 (t0) cc_final: 0.6061 (t0) REVERT: UUU 8 LYS cc_start: 0.9294 (ptmm) cc_final: 0.9021 (pttt) REVERT: ZZZ 11 PHE cc_start: 0.8835 (m-80) cc_final: 0.8249 (m-80) REVERT: ZZZ 41 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9393 (mm) REVERT: FFF 273 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7925 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7783 (pp20) cc_final: 0.7220 (pp20) REVERT: eee 20 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: jjj 47 SER cc_start: 0.8656 (m) cc_final: 0.8431 (p) REVERT: jjj 50 SER cc_start: 0.7598 (m) cc_final: 0.7341 (t) REVERT: ooo 29 VAL cc_start: 0.9731 (t) cc_final: 0.9498 (p) REVERT: LLL 20 GLU cc_start: 0.9632 (pt0) cc_final: 0.9382 (pm20) REVERT: QQQ 28 MET cc_start: 0.8386 (pmm) cc_final: 0.8100 (mmt) REVERT: QQQ 29 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7978 (p) REVERT: VVV 12 ASP cc_start: 0.9474 (m-30) cc_final: 0.8907 (p0) REVERT: VVV 22 ILE cc_start: 0.9164 (pp) cc_final: 0.8921 (pp) REVERT: aaa 11 PHE cc_start: 0.8645 (m-80) cc_final: 0.8248 (m-80) REVERT: aaa 15 GLN cc_start: 0.9213 (mt0) cc_final: 0.8990 (mm110) REVERT: BBB 111 ASP cc_start: 0.8501 (t70) cc_final: 0.8212 (t0) REVERT: GGG 261 GLU cc_start: 0.8681 (pm20) cc_final: 0.8474 (pm20) REVERT: GGG 262 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9032 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8286 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7737 (pp20) cc_final: 0.7234 (pp20) REVERT: GGG 355 ARG cc_start: 0.8547 (mtt180) cc_final: 0.8303 (mtt90) REVERT: fff 20 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: fff 44 LYS cc_start: 0.8860 (tmmm) cc_final: 0.8655 (tmtt) REVERT: kkk 47 SER cc_start: 0.8663 (m) cc_final: 0.8438 (p) REVERT: bbb 11 PHE cc_start: 0.8826 (m-80) cc_final: 0.8368 (m-80) REVERT: bbb 15 GLN cc_start: 0.9305 (mt0) cc_final: 0.9047 (mm110) REVERT: HHH 273 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7487 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7545 (pp20) cc_final: 0.7151 (pp20) REVERT: ggg 20 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: lll 40 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8784 (tttt) REVERT: qqq 20 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: XXX 5 ASP cc_start: 0.7327 (t0) cc_final: 0.5788 (t0) REVERT: XXX 8 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8685 (mptm) REVERT: XXX 12 ASP cc_start: 0.9509 (m-30) cc_final: 0.9036 (p0) REVERT: ccc 15 GLN cc_start: 0.9252 (mt0) cc_final: 0.8954 (mm110) REVERT: III 261 GLU cc_start: 0.8777 (pm20) cc_final: 0.8517 (pm20) REVERT: III 273 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8139 (mt-10) REVERT: III 353 GLU cc_start: 0.8041 (pp20) cc_final: 0.7553 (pp20) REVERT: III 355 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8570 (mtm-85) REVERT: hhh 20 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: mmm 29 VAL cc_start: 0.9374 (t) cc_final: 0.9115 (p) REVERT: rrr 20 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8771 (mp0) REVERT: OOO 28 MET cc_start: 0.9496 (ttp) cc_final: 0.9078 (pp-130) REVERT: YYY 5 ASP cc_start: 0.7391 (t0) cc_final: 0.6001 (t0) REVERT: ddd 15 GLN cc_start: 0.9295 (mt0) cc_final: 0.9014 (mm110) REVERT: ddd 24 TYR cc_start: 0.9482 (m-10) cc_final: 0.9181 (m-10) REVERT: ddd 40 LYS cc_start: 0.9541 (tttp) cc_final: 0.9317 (tttt) REVERT: JJJ 261 GLU cc_start: 0.8684 (pm20) cc_final: 0.8473 (pm20) REVERT: JJJ 273 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7830 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.7896 (pp20) cc_final: 0.7476 (pp20) REVERT: iii 20 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: nnn 40 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8887 (tttt) REVERT: nnn 50 SER cc_start: 0.7666 (t) cc_final: 0.7310 (m) outliers start: 43 outliers final: 28 residues processed: 426 average time/residue: 0.5920 time to fit residues: 283.6459 Evaluate side-chains 418 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 379 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain KKK residue 39 ILE Chi-restraints excluded: chain PPP residue 29 VAL Chi-restraints excluded: chain ZZZ residue 41 LEU Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 47 ILE Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain QQQ residue 29 VAL Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain VVV residue 20 GLU Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 47 ILE Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain RRR residue 29 VAL Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 20 GLU Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 47 ILE Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain XXX residue 20 GLU Chi-restraints excluded: chain ccc residue 21 MET Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain DDD residue 47 ILE Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain YYY residue 20 GLU Chi-restraints excluded: chain EEE residue 47 ILE Chi-restraints excluded: chain iii residue 20 GLU Chi-restraints excluded: chain nnn residue 40 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.037638 restraints weight = 67107.166| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.79 r_work: 0.2577 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20860 Z= 0.157 Angle : 0.637 10.360 28145 Z= 0.341 Chirality : 0.040 0.236 3320 Planarity : 0.003 0.031 3430 Dihedral : 3.386 16.366 2780 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.26 % Allowed : 30.92 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.16), residues: 2630 helix: 2.39 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : -0.15 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGIII 402 TYR 0.020 0.001 TYRKKK 24 PHE 0.014 0.001 PHECCC 43 TRP 0.004 0.001 TRPNNN 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (20860) covalent geometry : angle 0.63667 / 0.34 (28145) hydrogen bonds : bond 0.06478 / 4.22 ( 1611) hydrogen bonds : angle 3.60256 / 2.55 ( 4773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 388 time to evaluate : 0.716 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: KKK 20 GLU cc_start: 0.8875 (pp20) cc_final: 0.8659 (pp20) REVERT: KKK 21 MET cc_start: 0.7815 (mtp) cc_final: 0.7557 (mmm) REVERT: KKK 28 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.8859 (pp-130) REVERT: UUU 5 ASP cc_start: 0.6968 (t0) cc_final: 0.6006 (t0) REVERT: UUU 8 LYS cc_start: 0.9266 (ptmm) cc_final: 0.9046 (pttt) REVERT: ZZZ 41 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9400 (mm) REVERT: FFF 273 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7901 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7920 (pp20) cc_final: 0.7369 (pp20) REVERT: eee 20 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: jjj 20 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8403 (mt-10) REVERT: jjj 47 SER cc_start: 0.8723 (m) cc_final: 0.8500 (p) REVERT: jjj 50 SER cc_start: 0.7745 (m) cc_final: 0.7486 (t) REVERT: ooo 29 VAL cc_start: 0.9760 (t) cc_final: 0.9538 (p) REVERT: LLL 20 GLU cc_start: 0.9631 (pt0) cc_final: 0.9371 (pm20) REVERT: LLL 28 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6969 (pp-130) REVERT: QQQ 28 MET cc_start: 0.8401 (pmm) cc_final: 0.8107 (mmt) REVERT: VVV 8 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8740 (pmtt) REVERT: VVV 12 ASP cc_start: 0.9473 (m-30) cc_final: 0.8885 (p0) REVERT: VVV 22 ILE cc_start: 0.9206 (pp) cc_final: 0.8970 (pp) REVERT: aaa 11 PHE cc_start: 0.8718 (m-80) cc_final: 0.8304 (m-80) REVERT: BBB 111 ASP cc_start: 0.8546 (t70) cc_final: 0.8247 (t0) REVERT: GGG 261 GLU cc_start: 0.8724 (pm20) cc_final: 0.8519 (pm20) REVERT: GGG 262 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.9033 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8255 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7860 (pp20) cc_final: 0.7341 (pp20) REVERT: GGG 355 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8319 (mtt90) REVERT: fff 20 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: kkk 47 SER cc_start: 0.8795 (m) cc_final: 0.8553 (p) REVERT: bbb 11 PHE cc_start: 0.8831 (m-80) cc_final: 0.8353 (m-80) REVERT: bbb 15 GLN cc_start: 0.9298 (mt0) cc_final: 0.9030 (mm110) REVERT: HHH 273 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7483 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7703 (pp20) cc_final: 0.7302 (pp20) REVERT: ggg 20 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: lll 40 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8824 (tttt) REVERT: qqq 20 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8867 (mp0) REVERT: XXX 12 ASP cc_start: 0.9467 (m-30) cc_final: 0.9028 (p0) REVERT: ccc 15 GLN cc_start: 0.9260 (mt0) cc_final: 0.8964 (mm110) REVERT: III 261 GLU cc_start: 0.8800 (pm20) cc_final: 0.8544 (pm20) REVERT: III 273 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8085 (mt-10) REVERT: III 353 GLU cc_start: 0.8161 (pp20) cc_final: 0.7642 (pp20) REVERT: III 355 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8576 (mtm-85) REVERT: hhh 20 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: OOO 28 MET cc_start: 0.9512 (ttp) cc_final: 0.9099 (pp-130) REVERT: YYY 5 ASP cc_start: 0.7721 (t0) cc_final: 0.7406 (t0) REVERT: YYY 12 ASP cc_start: 0.9533 (m-30) cc_final: 0.9082 (p0) REVERT: YYY 22 ILE cc_start: 0.9194 (pp) cc_final: 0.8967 (pp) REVERT: YYY 32 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8971 (mp) REVERT: ddd 15 GLN cc_start: 0.9244 (mt0) cc_final: 0.8943 (mm110) REVERT: ddd 40 LYS cc_start: 0.9542 (tttp) cc_final: 0.9317 (tttt) REVERT: JJJ 261 GLU cc_start: 0.8698 (pm20) cc_final: 0.8480 (pm20) REVERT: JJJ 273 GLU cc_start: 0.8780 (mt-10) cc_final: 0.7950 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.8001 (pp20) cc_final: 0.7499 (pp20) REVERT: iii 20 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: iii 44 LYS cc_start: 0.8931 (tppt) cc_final: 0.8661 (tttm) REVERT: nnn 15 GLN cc_start: 0.9109 (mt0) cc_final: 0.8783 (mm-40) REVERT: nnn 40 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8798 (tttt) outliers start: 48 outliers final: 30 residues processed: 414 average time/residue: 0.6206 time to fit residues: 288.7954 Evaluate side-chains 413 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain PPP residue 29 VAL Chi-restraints excluded: chain UUU residue 20 GLU Chi-restraints excluded: chain ZZZ residue 41 LEU Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 47 ILE Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain LLL residue 28 MET Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain QQQ residue 37 ILE Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 47 ILE Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain RRR residue 29 VAL Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 20 GLU Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 47 ILE Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain XXX residue 20 GLU Chi-restraints excluded: chain ccc residue 21 MET Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain DDD residue 47 ILE Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain YYY residue 20 GLU Chi-restraints excluded: chain YYY residue 32 ILE Chi-restraints excluded: chain EEE residue 47 ILE Chi-restraints excluded: chain JJJ residue 316 THR Chi-restraints excluded: chain iii residue 20 GLU Chi-restraints excluded: chain nnn residue 40 LYS Chi-restraints excluded: chain sss residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 185 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 0.0020 chunk 233 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.039406 restraints weight = 66440.549| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.72 r_work: 0.2628 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20860 Z= 0.146 Angle : 0.652 11.490 28145 Z= 0.346 Chirality : 0.041 0.258 3320 Planarity : 0.003 0.030 3430 Dihedral : 3.378 16.605 2780 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.79 % Allowed : 31.25 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.16), residues: 2630 helix: 2.44 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : 0.00 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGGG 355 TYR 0.025 0.001 TYRddd 24 PHE 0.011 0.001 PHEAAA 43 TRP 0.006 0.000 TRPNNN 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (20860) covalent geometry : angle 0.65193 / 0.35 (28145) hydrogen bonds : bond 0.06175 / 4.02 ( 1611) hydrogen bonds : angle 3.53023 / 2.51 ( 4773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 0.860 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: KKK 20 GLU cc_start: 0.8843 (pp20) cc_final: 0.8615 (pp20) REVERT: KKK 21 MET cc_start: 0.7809 (mtp) cc_final: 0.7551 (mmm) REVERT: KKK 28 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8843 (pp-130) REVERT: ZZZ 41 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9410 (mm) REVERT: FFF 273 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7929 (mt-10) REVERT: FFF 353 GLU cc_start: 0.7958 (pp20) cc_final: 0.7390 (pp20) REVERT: eee 20 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: jjj 47 SER cc_start: 0.8678 (m) cc_final: 0.8450 (p) REVERT: ooo 29 VAL cc_start: 0.9760 (t) cc_final: 0.9532 (p) REVERT: LLL 28 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7056 (pp-130) REVERT: QQQ 28 MET cc_start: 0.8515 (pmm) cc_final: 0.8134 (mmt) REVERT: VVV 12 ASP cc_start: 0.9446 (m-30) cc_final: 0.8927 (p0) REVERT: VVV 22 ILE cc_start: 0.9224 (pp) cc_final: 0.8994 (pp) REVERT: aaa 20 GLU cc_start: 0.8851 (pp20) cc_final: 0.8625 (pp20) REVERT: aaa 24 TYR cc_start: 0.9376 (m-10) cc_final: 0.9167 (m-10) REVERT: BBB 111 ASP cc_start: 0.8525 (t70) cc_final: 0.8261 (t0) REVERT: GGG 261 GLU cc_start: 0.8670 (pm20) cc_final: 0.8459 (pm20) REVERT: GGG 262 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9062 (ptmm) REVERT: GGG 273 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8247 (mt-10) REVERT: GGG 353 GLU cc_start: 0.7871 (pp20) cc_final: 0.7326 (pp20) REVERT: GGG 355 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8236 (mtt90) REVERT: fff 20 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: fff 44 LYS cc_start: 0.8854 (tmmm) cc_final: 0.8653 (tmtt) REVERT: kkk 47 SER cc_start: 0.8716 (m) cc_final: 0.8483 (p) REVERT: bbb 11 PHE cc_start: 0.8827 (m-80) cc_final: 0.8358 (m-80) REVERT: bbb 15 GLN cc_start: 0.9297 (mt0) cc_final: 0.9031 (mm110) REVERT: HHH 273 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7510 (mt-10) REVERT: HHH 353 GLU cc_start: 0.7701 (pp20) cc_final: 0.7292 (pp20) REVERT: ggg 20 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: lll 40 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8793 (tttt) REVERT: XXX 12 ASP cc_start: 0.9448 (m-30) cc_final: 0.9007 (p0) REVERT: ccc 15 GLN cc_start: 0.9260 (mt0) cc_final: 0.8970 (mm110) REVERT: III 261 GLU cc_start: 0.8769 (pm20) cc_final: 0.8507 (pm20) REVERT: III 273 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8133 (mt-10) REVERT: III 353 GLU cc_start: 0.8172 (pp20) cc_final: 0.7649 (pp20) REVERT: III 355 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: hhh 20 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: OOO 28 MET cc_start: 0.9516 (ttp) cc_final: 0.9153 (pp-130) REVERT: YYY 12 ASP cc_start: 0.9497 (m-30) cc_final: 0.9053 (p0) REVERT: YYY 32 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8940 (mp) REVERT: ddd 15 GLN cc_start: 0.9270 (mt0) cc_final: 0.8989 (mm110) REVERT: ddd 20 GLU cc_start: 0.8301 (pp20) cc_final: 0.8018 (pp20) REVERT: ddd 40 LYS cc_start: 0.9552 (tttp) cc_final: 0.9326 (tttt) REVERT: JJJ 261 GLU cc_start: 0.8686 (pm20) cc_final: 0.8476 (pm20) REVERT: JJJ 273 GLU cc_start: 0.8734 (mt-10) cc_final: 0.7857 (mt-10) REVERT: JJJ 353 GLU cc_start: 0.8018 (pp20) cc_final: 0.7520 (pp20) REVERT: iii 20 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: iii 44 LYS cc_start: 0.8900 (tppt) cc_final: 0.8633 (tttm) REVERT: nnn 15 GLN cc_start: 0.9111 (mt0) cc_final: 0.8797 (mm-40) REVERT: nnn 40 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8827 (tttt) REVERT: nnn 50 SER cc_start: 0.7711 (t) cc_final: 0.7353 (m) REVERT: sss 12 ASP cc_start: 0.9548 (m-30) cc_final: 0.9300 (p0) outliers start: 38 outliers final: 29 residues processed: 419 average time/residue: 0.6425 time to fit residues: 303.4513 Evaluate side-chains 422 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 28 MET Chi-restraints excluded: chain PPP residue 29 VAL Chi-restraints excluded: chain UUU residue 20 GLU Chi-restraints excluded: chain ZZZ residue 41 LEU Chi-restraints excluded: chain AAA residue 3 VAL Chi-restraints excluded: chain AAA residue 47 ILE Chi-restraints excluded: chain FFF residue 352 VAL Chi-restraints excluded: chain FFF residue 371 CYS Chi-restraints excluded: chain eee residue 20 GLU Chi-restraints excluded: chain LLL residue 28 MET Chi-restraints excluded: chain QQQ residue 30 VAL Chi-restraints excluded: chain BBB residue 3 VAL Chi-restraints excluded: chain BBB residue 47 ILE Chi-restraints excluded: chain GGG residue 262 LYS Chi-restraints excluded: chain GGG residue 371 CYS Chi-restraints excluded: chain fff residue 20 GLU Chi-restraints excluded: chain fff residue 37 ILE Chi-restraints excluded: chain RRR residue 29 VAL Chi-restraints excluded: chain RRR residue 30 VAL Chi-restraints excluded: chain WWW residue 20 GLU Chi-restraints excluded: chain WWW residue 32 ILE Chi-restraints excluded: chain CCC residue 47 ILE Chi-restraints excluded: chain HHH residue 371 CYS Chi-restraints excluded: chain ggg residue 20 GLU Chi-restraints excluded: chain qqq residue 20 GLU Chi-restraints excluded: chain SSS residue 29 VAL Chi-restraints excluded: chain SSS residue 30 VAL Chi-restraints excluded: chain XXX residue 20 GLU Chi-restraints excluded: chain ccc residue 20 GLU Chi-restraints excluded: chain ccc residue 21 MET Chi-restraints excluded: chain DDD residue 3 VAL Chi-restraints excluded: chain DDD residue 47 ILE Chi-restraints excluded: chain III residue 371 CYS Chi-restraints excluded: chain hhh residue 20 GLU Chi-restraints excluded: chain TTT residue 29 VAL Chi-restraints excluded: chain YYY residue 20 GLU Chi-restraints excluded: chain YYY residue 32 ILE Chi-restraints excluded: chain EEE residue 47 ILE Chi-restraints excluded: chain iii residue 20 GLU Chi-restraints excluded: chain nnn residue 40 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 100 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.039311 restraints weight = 66641.383| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.79 r_work: 0.2609 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20860 Z= 0.152 Angle : 0.667 11.721 28145 Z= 0.355 Chirality : 0.041 0.241 3320 Planarity : 0.003 0.031 3430 Dihedral : 3.374 16.151 2780 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.93 % Allowed : 31.48 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.16), residues: 2630 helix: 2.44 (0.11), residues: 2190 sheet: None (None), residues: 0 loop : 0.18 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGGGG 355 TYR 0.026 0.001 TYRddd 24 PHE 0.012 0.001 PHECCC 43 TRP 0.005 0.000 TRPNNN 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (20860) covalent geometry : angle 0.66704 / 0.35 (28145) hydrogen bonds : bond 0.06197 / 4.04 ( 1611) hydrogen bonds : angle 3.59255 / 2.54 ( 4773) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7251.01 seconds wall clock time: 123 minutes 42.80 seconds (7422.80 seconds total)