Starting phenix.real_space_refine on Fri Aug 7 12:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2026/8x2y_38022.cif" } resolution = 4.1 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= -0.020 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5443 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 22 5.16 5 C 10104 2.51 5 N 3123 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17396 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "K" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2357 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 465 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain breaks: 1 Chain: "M" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1831 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Time building chain proxies: 3.20, per 1000 atoms: 0.18 Number of scatterers: 17396 At special positions: 0 Unit cell: (152.88, 137.28, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 290 15.00 O 3857 8.00 N 3123 7.00 C 10104 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: 1.06 Conformation dependent library (CDL) restraints added in 592.1 milliseconds 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 7 sheets defined 57.7% alpha, 2.5% beta 143 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.116A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.626A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.748A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.450A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.063A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.570A pdb=" N ILE C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 66 removed outlier: 3.988A pdb=" N LEU C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 80 through 86 Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.131A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 60 through 87 Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.872A pdb=" N LEU D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.696A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.654A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 5.239A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 33 through 41 removed outlier: 5.152A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 27 through 39 removed outlier: 3.882A pdb=" N ILE G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 62 removed outlier: 3.723A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 68 through 74 removed outlier: 3.756A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS G 73 " --> pdb=" O GLY G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.524A pdb=" N LEU G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.823A pdb=" N LEU H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.739A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 191 removed outlier: 4.125A pdb=" N THR K 190 " --> pdb=" O PRO K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 removed outlier: 3.657A pdb=" N ARG K 215 " --> pdb=" O TYR K 211 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS K 216 " --> pdb=" O GLU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 256 removed outlier: 3.964A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 327 Processing helix chain 'K' and resid 327 through 332 removed outlier: 3.554A pdb=" N GLU K 331 " --> pdb=" O LEU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 363 removed outlier: 3.651A pdb=" N TRP K 353 " --> pdb=" O TYR K 349 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 359 " --> pdb=" O ASP K 355 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 377 removed outlier: 3.636A pdb=" N SER K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 386 removed outlier: 3.610A pdb=" N ILE K 384 " --> pdb=" O THR K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 415 Processing helix chain 'L' and resid 6 through 31 removed outlier: 3.572A pdb=" N ALA L 13 " --> pdb=" O GLU L 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU L 24 " --> pdb=" O GLN L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 44 removed outlier: 3.902A pdb=" N GLU L 35 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS L 39 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 134 removed outlier: 3.618A pdb=" N TYR M 133 " --> pdb=" O TRP M 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP M 134 " --> pdb=" O ASN M 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 130 through 134' Processing helix chain 'M' and resid 153 through 158 removed outlier: 3.875A pdb=" N CYS M 158 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 removed outlier: 3.675A pdb=" N ASP M 168 " --> pdb=" O ASP M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 186 through 190 Processing helix chain 'M' and resid 193 through 201 removed outlier: 3.551A pdb=" N GLU M 197 " --> pdb=" O CYS M 193 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA M 199 " --> pdb=" O SER M 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE M 200 " --> pdb=" O PHE M 196 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.982A pdb=" N LEU M 224 " --> pdb=" O LEU M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 243 removed outlier: 4.424A pdb=" N GLU M 241 " --> pdb=" O GLN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 283 removed outlier: 3.889A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 283 " --> pdb=" O TRP M 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 277 through 283' Processing helix chain 'M' and resid 332 through 339 removed outlier: 3.725A pdb=" N ALA M 336 " --> pdb=" O GLN M 332 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN M 339 " --> pdb=" O ARG M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 361 removed outlier: 3.709A pdb=" N LEU M 347 " --> pdb=" O ASN M 343 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 removed outlier: 4.238A pdb=" N VAL M 373 " --> pdb=" O ASP M 370 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS M 374 " --> pdb=" O GLN M 371 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE M 375 " --> pdb=" O ARG M 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.479A pdb=" N VAL N 6 " --> pdb=" O ASP N 2 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.838A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 removed outlier: 3.657A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 45 Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 76 through 81 removed outlier: 3.570A pdb=" N SER N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 102 removed outlier: 4.664A pdb=" N LEU N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR N 92 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE N 95 " --> pdb=" O ASN N 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 112 removed outlier: 4.158A pdb=" N LYS N 106 " --> pdb=" O ASN N 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.821A pdb=" N THR C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.285A pdb=" N THR G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'K' and resid 170 through 172 removed outlier: 4.001A pdb=" N MET K 172 " --> pdb=" O TYR K 175 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR K 175 " --> pdb=" O MET K 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 234 through 239 removed outlier: 3.601A pdb=" N THR K 277 " --> pdb=" O SER K 235 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE K 237 " --> pdb=" O CYS K 275 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 290 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG K 278 " --> pdb=" O LEU K 286 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU K 286 " --> pdb=" O ARG K 278 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3309 1.33 - 1.45: 5533 1.45 - 1.57: 8854 1.57 - 1.69: 580 1.69 - 1.81: 34 Bond restraints: 18310 Sorted by residual: bond pdb=" C LYS K 339 " pdb=" N PRO K 340 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.28e-02 6.10e+03 3.02e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.30e+01 bond pdb=" C1' DT I 119 " pdb=" N1 DT I 119 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA THR C 61 " pdb=" C THR C 61 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" C3' DC J 193 " pdb=" O3' DC J 193 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.70e+01 ... (remaining 18305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 23806 1.92 - 3.84: 1909 3.84 - 5.76: 166 5.76 - 7.69: 52 7.69 - 9.61: 15 Bond angle restraints: 25948 Sorted by residual: angle pdb=" O4' DA I 29 " pdb=" C4' DA I 29 " pdb=" C3' DA I 29 " ideal model delta sigma weight residual 106.00 101.96 4.04 6.00e-01 2.78e+00 4.53e+01 angle pdb=" O4' DT I 118 " pdb=" C4' DT I 118 " pdb=" C3' DT I 118 " ideal model delta sigma weight residual 106.00 102.03 3.97 6.00e-01 2.78e+00 4.38e+01 angle pdb=" O4' DT I 117 " pdb=" C1' DT I 117 " pdb=" N1 DT I 117 " ideal model delta sigma weight residual 108.00 112.39 -4.39 7.00e-01 2.04e+00 3.93e+01 angle pdb=" C4' DA I 29 " pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " ideal model delta sigma weight residual 103.10 98.26 4.84 9.00e-01 1.23e+00 2.89e+01 angle pdb=" O4' DA I 126 " pdb=" C1' DA I 126 " pdb=" N9 DA I 126 " ideal model delta sigma weight residual 108.00 111.73 -3.73 7.00e-01 2.04e+00 2.84e+01 ... (remaining 25943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7555 17.89 - 35.79: 1314 35.79 - 53.68: 1171 53.68 - 71.58: 339 71.58 - 89.47: 21 Dihedral angle restraints: 10400 sinusoidal: 6266 harmonic: 4134 Sorted by residual: dihedral pdb=" CA LYS K 398 " pdb=" C LYS K 398 " pdb=" N GLY K 399 " pdb=" CA GLY K 399 " ideal model delta harmonic sigma weight residual -180.00 -136.63 -43.37 0 5.00e+00 4.00e-02 7.52e+01 dihedral pdb=" CA HIS G 38 " pdb=" C HIS G 38 " pdb=" N ALA G 39 " pdb=" CA ALA G 39 " ideal model delta harmonic sigma weight residual 180.00 142.06 37.94 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA PRO K 223 " pdb=" C PRO K 223 " pdb=" N PRO K 224 " pdb=" CA PRO K 224 " ideal model delta harmonic sigma weight residual -180.00 -144.72 -35.28 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 10397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1820 0.050 - 0.100: 828 0.100 - 0.149: 235 0.149 - 0.199: 33 0.199 - 0.249: 8 Chirality restraints: 2924 Sorted by residual: chirality pdb=" CB ILE K 368 " pdb=" CA ILE K 368 " pdb=" CG1 ILE K 368 " pdb=" CG2 ILE K 368 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" P DA J 197 " pdb=" OP1 DA J 197 " pdb=" OP2 DA J 197 " pdb=" O5' DA J 197 " both_signs ideal model delta sigma weight residual True 2.34 -2.58 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2921 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 336 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO K 337 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO K 337 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 337 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " -0.030 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR F 98 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 38 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C HIS G 38 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS G 38 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA G 39 " 0.015 2.00e-02 2.50e+03 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4432 2.81 - 3.33: 15729 3.33 - 3.85: 33369 3.85 - 4.38: 37178 4.38 - 4.90: 52049 Nonbonded interactions: 142757 Sorted by model distance: nonbonded pdb=" OG1 THR C 102 " pdb=" O THR F 96 " model vdw 2.284 3.040 nonbonded pdb=" O LEU N 7 " pdb=" OG1 THR N 10 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.289 3.040 nonbonded pdb=" O ILE C 51 " pdb=" OG1 THR C 54 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR K 185 " pdb=" O LEU K 253 " model vdw 2.301 3.040 ... (remaining 142752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 0.070 18310 Z= 0.604 Angle : 1.083 9.607 25948 Z= 0.809 Chirality : 0.060 0.249 2924 Planarity : 0.007 0.074 2268 Dihedral : 25.181 89.469 7716 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.72 % Favored : 92.21 % Rotamer: Outliers : 0.80 % Allowed : 5.30 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.37 % 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: -4.42 (0.18), residues: 1373 helix: -3.19 (0.14), residues: 650 sheet: -2.11 (1.07), residues: 26 loop : -2.69 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 63 TYR 0.043 0.003 TYR F 98 PHE 0.019 0.002 PHE K 271 TRP 0.035 0.003 TRP K 353 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.60 (18310) covalent geometry : angle 1.08337 / 0.81 (25948) hydrogen bonds : bond 0.17855 / 11.79 ( 821) hydrogen bonds : angle 7.17455 / 5.17 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 555 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8159 (p) cc_final: 0.7952 (p) REVERT: A 51 ILE cc_start: 0.7838 (mm) cc_final: 0.6986 (mm) REVERT: A 59 GLU cc_start: 0.8075 (pm20) cc_final: 0.7831 (pm20) REVERT: A 125 LYS cc_start: 0.8409 (tppt) cc_final: 0.7904 (tppt) REVERT: B 46 ILE cc_start: 0.7029 (mm) cc_final: 0.6792 (mm) REVERT: B 74 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 38 GLU cc_start: 0.6419 (tp30) cc_final: 0.6082 (tp30) REVERT: D 57 ILE cc_start: 0.7453 (mm) cc_final: 0.6986 (tp) REVERT: D 74 GLU cc_start: 0.7390 (tp30) cc_final: 0.6798 (tp30) REVERT: D 104 ILE cc_start: 0.7634 (tp) cc_final: 0.7252 (tp) REVERT: E 46 VAL cc_start: 0.7293 (p) cc_final: 0.7038 (m) REVERT: E 62 ILE cc_start: 0.6465 (tt) cc_final: 0.5901 (tp) REVERT: E 78 PHE cc_start: 0.8033 (m-10) cc_final: 0.6288 (m-10) REVERT: F 82 THR cc_start: 0.7623 (t) cc_final: 0.6858 (p) REVERT: G 24 LEU cc_start: 0.8512 (mt) cc_final: 0.7913 (mt) REVERT: G 67 LEU cc_start: 0.7687 (mt) cc_final: 0.6914 (mt) REVERT: H 63 SER cc_start: 0.8015 (t) cc_final: 0.7543 (p) REVERT: H 96 GLU cc_start: 0.7801 (pm20) cc_final: 0.7512 (pm20) REVERT: H 104 ILE cc_start: 0.8452 (tp) cc_final: 0.8240 (tp) REVERT: K 160 GLU cc_start: 0.7539 (pm20) cc_final: 0.6084 (pm20) REVERT: K 167 LEU cc_start: 0.8712 (mm) cc_final: 0.8009 (tp) REVERT: K 197 ILE cc_start: 0.8157 (mm) cc_final: 0.7807 (mm) REVERT: K 236 PHE cc_start: 0.6325 (m-80) cc_final: 0.5509 (m-80) REVERT: K 275 CYS cc_start: 0.7081 (m) cc_final: 0.6278 (t) REVERT: K 276 MET cc_start: 0.5782 (tpt) cc_final: 0.5557 (tpt) REVERT: K 310 GLN cc_start: 0.7077 (pt0) cc_final: 0.6779 (mt0) REVERT: K 350 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7525 (mtt90) REVERT: K 364 HIS cc_start: 0.6767 (t-90) cc_final: 0.6400 (t-90) REVERT: K 372 GLU cc_start: 0.8469 (tt0) cc_final: 0.8010 (tt0) REVERT: M 141 PHE cc_start: 0.7923 (p90) cc_final: 0.7624 (p90) REVERT: M 215 LEU cc_start: 0.4449 (mp) cc_final: 0.3553 (mp) REVERT: M 259 MET cc_start: 0.5054 (pmm) cc_final: 0.4785 (pmm) REVERT: M 265 ILE cc_start: 0.8188 (pt) cc_final: 0.7944 (tp) REVERT: M 278 TYR cc_start: 0.6380 (t80) cc_final: 0.6141 (t80) REVERT: N 23 TYR cc_start: 0.7272 (t80) cc_final: 0.7041 (t80) REVERT: N 97 ILE cc_start: 0.7171 (mt) cc_final: 0.6957 (mt) outliers start: 10 outliers final: 1 residues processed: 557 average time/residue: 0.1679 time to fit residues: 130.6349 Evaluate side-chains 436 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 76 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN K 285 HIS ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.106175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.089127 restraints weight = 58283.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091648 restraints weight = 30849.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.093286 restraints weight = 19363.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094335 restraints weight = 13885.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094988 restraints weight = 11039.974| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18310 Z= 0.187 Angle : 0.846 10.928 25948 Z= 0.469 Chirality : 0.050 0.226 2924 Planarity : 0.006 0.057 2268 Dihedral : 29.761 88.549 4818 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.56 % Allowed : 5.62 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.39 (0.20), residues: 1373 helix: -1.92 (0.17), residues: 686 sheet: -2.11 (0.98), residues: 26 loop : -2.59 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 128 TYR 0.031 0.002 TYR F 98 PHE 0.026 0.002 PHE E 54 TRP 0.012 0.002 TRP K 247 HIS 0.010 0.001 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (18310) covalent geometry : angle 0.84574 / 0.47 (25948) hydrogen bonds : bond 0.06171 / 4.06 ( 821) hydrogen bonds : angle 5.22901 / 3.75 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 479 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8204 (mm) cc_final: 0.8004 (mm) REVERT: A 97 GLU cc_start: 0.7455 (tp30) cc_final: 0.7253 (tp30) REVERT: A 125 LYS cc_start: 0.8435 (tppt) cc_final: 0.7945 (tppt) REVERT: B 37 LEU cc_start: 0.8770 (tp) cc_final: 0.8313 (tp) REVERT: B 39 ARG cc_start: 0.7354 (tpp80) cc_final: 0.6860 (tpp80) REVERT: C 74 ASP cc_start: 0.7651 (t0) cc_final: 0.7330 (t0) REVERT: D 43 TYR cc_start: 0.7926 (m-80) cc_final: 0.7462 (m-80) REVERT: D 57 ILE cc_start: 0.7236 (mm) cc_final: 0.6881 (tp) REVERT: D 71 ASP cc_start: 0.7413 (m-30) cc_final: 0.7053 (m-30) REVERT: D 74 GLU cc_start: 0.7173 (tp30) cc_final: 0.6897 (tp30) REVERT: D 98 GLN cc_start: 0.7775 (tp40) cc_final: 0.7222 (tp40) REVERT: D 102 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7444 (ttm110) REVERT: F 27 GLN cc_start: 0.7444 (mp-120) cc_final: 0.5676 (mp10) REVERT: F 60 SER cc_start: 0.8357 (m) cc_final: 0.8100 (p) REVERT: F 63 GLU cc_start: 0.6661 (tp30) cc_final: 0.5874 (tp30) REVERT: F 78 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7359 (ptp90) REVERT: F 82 THR cc_start: 0.7783 (t) cc_final: 0.6834 (p) REVERT: H 63 SER cc_start: 0.8018 (t) cc_final: 0.7514 (p) REVERT: H 74 GLU cc_start: 0.7588 (tp30) cc_final: 0.7204 (tp30) REVERT: K 167 LEU cc_start: 0.8602 (mm) cc_final: 0.8121 (tp) REVERT: K 238 GLU cc_start: 0.6693 (tt0) cc_final: 0.5897 (mt-10) REVERT: K 250 ASN cc_start: 0.7207 (p0) cc_final: 0.6968 (p0) REVERT: K 269 ASP cc_start: 0.8626 (m-30) cc_final: 0.8363 (m-30) REVERT: K 274 TYR cc_start: 0.7209 (m-10) cc_final: 0.6981 (m-10) REVERT: K 275 CYS cc_start: 0.7104 (m) cc_final: 0.6887 (t) REVERT: K 364 HIS cc_start: 0.6729 (t-90) cc_final: 0.6412 (t-90) REVERT: M 141 PHE cc_start: 0.7878 (p90) cc_final: 0.7620 (p90) REVERT: M 234 LEU cc_start: 0.6856 (mt) cc_final: 0.6648 (mt) REVERT: M 265 ILE cc_start: 0.8302 (pt) cc_final: 0.7952 (tp) REVERT: N 31 ASN cc_start: 0.8321 (m110) cc_final: 0.7746 (t0) outliers start: 7 outliers final: 1 residues processed: 483 average time/residue: 0.1675 time to fit residues: 114.2489 Evaluate side-chains 426 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 146 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN K 285 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.105785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088908 restraints weight = 58713.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091370 restraints weight = 31247.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092953 restraints weight = 19706.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093994 restraints weight = 14212.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094687 restraints weight = 11332.133| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18310 Z= 0.193 Angle : 0.793 10.125 25948 Z= 0.445 Chirality : 0.049 0.232 2924 Planarity : 0.006 0.072 2268 Dihedral : 29.567 89.038 4818 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.02 (0.20), residues: 1373 helix: -1.52 (0.17), residues: 694 sheet: -1.93 (1.08), residues: 26 loop : -2.54 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 39 TYR 0.029 0.002 TYR F 98 PHE 0.020 0.002 PHE K 236 TRP 0.046 0.003 TRP K 353 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (18310) covalent geometry : angle 0.79265 / 0.45 (25948) hydrogen bonds : bond 0.05860 / 3.82 ( 821) hydrogen bonds : angle 4.83311 / 3.48 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 503 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7292 (mtt90) cc_final: 0.7074 (mtt90) REVERT: A 121 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8369 (ptmm) REVERT: A 125 LYS cc_start: 0.8406 (tppt) cc_final: 0.7946 (tppt) REVERT: B 37 LEU cc_start: 0.8826 (tp) cc_final: 0.8344 (tp) REVERT: B 39 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7062 (mmt90) REVERT: B 55 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7822 (mtp85) REVERT: C 74 ASP cc_start: 0.7798 (t0) cc_final: 0.7562 (t0) REVERT: D 42 SER cc_start: 0.8672 (m) cc_final: 0.8201 (p) REVERT: D 71 ASP cc_start: 0.7486 (m-30) cc_final: 0.7177 (m-30) REVERT: D 98 GLN cc_start: 0.7897 (tp40) cc_final: 0.7010 (tp40) REVERT: D 102 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7505 (ttm110) REVERT: E 65 LEU cc_start: 0.7932 (tt) cc_final: 0.7708 (tp) REVERT: E 78 PHE cc_start: 0.7970 (m-10) cc_final: 0.7514 (m-10) REVERT: F 27 GLN cc_start: 0.7925 (mp-120) cc_final: 0.7577 (mp10) REVERT: F 49 LEU cc_start: 0.7018 (tp) cc_final: 0.6552 (tp) REVERT: F 53 GLU cc_start: 0.7608 (mp0) cc_final: 0.7092 (mp0) REVERT: F 63 GLU cc_start: 0.6942 (tp30) cc_final: 0.6526 (tp30) REVERT: F 78 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7512 (ptp90) REVERT: F 82 THR cc_start: 0.8062 (t) cc_final: 0.7117 (p) REVERT: F 88 TYR cc_start: 0.6671 (m-10) cc_final: 0.6276 (m-10) REVERT: G 56 VAL cc_start: 0.8112 (t) cc_final: 0.7874 (m) REVERT: G 67 LEU cc_start: 0.7837 (mt) cc_final: 0.7123 (mt) REVERT: G 80 ILE cc_start: 0.7499 (tt) cc_final: 0.7193 (tt) REVERT: G 81 THR cc_start: 0.8175 (m) cc_final: 0.7636 (p) REVERT: G 87 LEU cc_start: 0.7294 (tp) cc_final: 0.6829 (tp) REVERT: H 74 GLU cc_start: 0.7544 (tp30) cc_final: 0.7197 (tp30) REVERT: K 167 LEU cc_start: 0.8576 (mm) cc_final: 0.8179 (tp) REVERT: K 238 GLU cc_start: 0.6805 (tt0) cc_final: 0.5644 (mt-10) REVERT: K 269 ASP cc_start: 0.8517 (m-30) cc_final: 0.8295 (m-30) REVERT: K 274 TYR cc_start: 0.7392 (m-10) cc_final: 0.6967 (m-10) REVERT: K 364 HIS cc_start: 0.7057 (t-90) cc_final: 0.6647 (t-90) REVERT: L 40 GLU cc_start: 0.7547 (tp30) cc_final: 0.7013 (tp30) REVERT: L 44 PHE cc_start: 0.7722 (m-10) cc_final: 0.7199 (m-10) REVERT: M 141 PHE cc_start: 0.7955 (p90) cc_final: 0.7481 (p90) REVERT: N 31 ASN cc_start: 0.8327 (m110) cc_final: 0.7768 (t0) REVERT: N 97 ILE cc_start: 0.7740 (mt) cc_final: 0.7477 (mt) outliers start: 2 outliers final: 1 residues processed: 504 average time/residue: 0.1668 time to fit residues: 118.2629 Evaluate side-chains 452 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 451 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 144 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN C 38 HIS D 66 ASN E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084985 restraints weight = 58376.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.087280 restraints weight = 31820.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.088757 restraints weight = 20426.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089740 restraints weight = 14935.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090310 restraints weight = 12131.690| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18310 Z= 0.307 Angle : 1.008 12.273 25948 Z= 0.548 Chirality : 0.057 0.295 2924 Planarity : 0.008 0.133 2268 Dihedral : 29.444 89.538 4818 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.16 % Allowed : 7.38 % Favored : 92.46 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.30 % 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: -2.79 (0.21), residues: 1373 helix: -1.18 (0.18), residues: 700 sheet: -2.32 (1.06), residues: 26 loop : -2.61 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 350 TYR 0.049 0.003 TYR F 98 PHE 0.032 0.004 PHE A 104 TRP 0.018 0.002 TRP K 353 HIS 0.010 0.002 HIS M 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.31 (18310) covalent geometry : angle 1.00832 / 0.55 (25948) hydrogen bonds : bond 0.07738 / 5.00 ( 821) hydrogen bonds : angle 4.83611 / 3.47 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 535 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8360 (m-80) cc_final: 0.8126 (m-10) REVERT: A 57 SER cc_start: 0.8265 (t) cc_final: 0.7876 (p) REVERT: A 59 GLU cc_start: 0.8592 (pm20) cc_final: 0.8343 (pm20) REVERT: A 62 ILE cc_start: 0.8903 (mm) cc_final: 0.8664 (mt) REVERT: A 97 GLU cc_start: 0.7831 (tp30) cc_final: 0.7454 (tp30) REVERT: A 125 LYS cc_start: 0.8649 (tppt) cc_final: 0.8221 (tppt) REVERT: B 31 LYS cc_start: 0.8424 (tppp) cc_final: 0.8141 (tppp) REVERT: B 39 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7915 (mmm-85) REVERT: B 88 TYR cc_start: 0.8807 (m-10) cc_final: 0.8366 (m-10) REVERT: C 63 GLU cc_start: 0.8049 (pp20) cc_final: 0.7675 (pp20) REVERT: C 113 ASN cc_start: 0.7790 (p0) cc_final: 0.7509 (p0) REVERT: D 37 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7233 (mtpp) REVERT: D 42 SER cc_start: 0.8486 (m) cc_final: 0.8259 (p) REVERT: D 57 ILE cc_start: 0.8698 (mm) cc_final: 0.8378 (mm) REVERT: D 71 ASP cc_start: 0.7565 (m-30) cc_final: 0.7228 (m-30) REVERT: D 74 GLU cc_start: 0.7383 (tp30) cc_final: 0.6874 (tp30) REVERT: D 88 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8460 (mtpp) REVERT: D 98 GLN cc_start: 0.8103 (tp40) cc_final: 0.7848 (tp40) REVERT: D 102 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7567 (ttm110) REVERT: D 108 GLU cc_start: 0.7415 (pp20) cc_final: 0.7088 (pp20) REVERT: D 116 GLU cc_start: 0.7962 (pp20) cc_final: 0.7484 (pp20) REVERT: D 118 THR cc_start: 0.7969 (m) cc_final: 0.7707 (m) REVERT: D 119 ARG cc_start: 0.8059 (tmm160) cc_final: 0.7815 (tmm-80) REVERT: E 59 GLU cc_start: 0.8239 (tp30) cc_final: 0.8032 (tp30) REVERT: E 70 LEU cc_start: 0.8558 (mm) cc_final: 0.8141 (tp) REVERT: F 49 LEU cc_start: 0.7742 (tp) cc_final: 0.7484 (tt) REVERT: F 50 ILE cc_start: 0.8489 (pt) cc_final: 0.8129 (tp) REVERT: F 61 PHE cc_start: 0.8576 (t80) cc_final: 0.8371 (t80) REVERT: F 88 TYR cc_start: 0.7425 (m-10) cc_final: 0.6794 (m-10) REVERT: G 44 ARG cc_start: 0.7230 (tpt90) cc_final: 0.6587 (tpt170) REVERT: G 56 VAL cc_start: 0.8152 (t) cc_final: 0.7882 (t) REVERT: G 67 LEU cc_start: 0.8136 (mt) cc_final: 0.7633 (mt) REVERT: G 87 LEU cc_start: 0.7561 (tp) cc_final: 0.6492 (tp) REVERT: G 93 ASP cc_start: 0.7252 (t0) cc_final: 0.6792 (t0) REVERT: G 113 ASN cc_start: 0.8991 (t0) cc_final: 0.8695 (t0) REVERT: H 48 LEU cc_start: 0.8471 (tp) cc_final: 0.8067 (tt) REVERT: H 55 THR cc_start: 0.8737 (m) cc_final: 0.8365 (p) REVERT: H 65 LEU cc_start: 0.8316 (mm) cc_final: 0.7930 (mt) REVERT: H 74 GLU cc_start: 0.7733 (tp30) cc_final: 0.7448 (tp30) REVERT: H 118 THR cc_start: 0.8646 (t) cc_final: 0.8432 (p) REVERT: K 178 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7439 (mm-30) REVERT: K 221 ARG cc_start: 0.5570 (ttt180) cc_final: 0.4423 (ttt180) REVERT: K 353 TRP cc_start: 0.8489 (m-90) cc_final: 0.7931 (m-90) REVERT: K 406 ASN cc_start: 0.7687 (p0) cc_final: 0.7408 (p0) REVERT: L 40 GLU cc_start: 0.7944 (tp30) cc_final: 0.7668 (tp30) REVERT: M 234 LEU cc_start: 0.6992 (mt) cc_final: 0.6778 (mt) REVERT: N 8 GLU cc_start: 0.8354 (mp0) cc_final: 0.8046 (mp0) REVERT: N 31 ASN cc_start: 0.7976 (m110) cc_final: 0.7566 (t0) REVERT: N 96 LEU cc_start: 0.8336 (pp) cc_final: 0.8046 (pp) outliers start: 2 outliers final: 1 residues processed: 536 average time/residue: 0.1749 time to fit residues: 130.3016 Evaluate side-chains 477 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN H 59 GLN H 98 GLN K 285 HIS K 301 ASN K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN N 107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.103443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.086476 restraints weight = 58008.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088790 restraints weight = 31231.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090295 restraints weight = 20023.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091294 restraints weight = 14594.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091895 restraints weight = 11821.343| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18310 Z= 0.192 Angle : 0.816 13.185 25948 Z= 0.450 Chirality : 0.050 0.222 2924 Planarity : 0.006 0.073 2268 Dihedral : 29.388 89.360 4818 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.64 (0.21), residues: 1373 helix: -1.07 (0.18), residues: 703 sheet: -2.62 (1.01), residues: 26 loop : -2.50 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 428 TYR 0.029 0.002 TYR K 352 PHE 0.029 0.002 PHE K 237 TRP 0.016 0.002 TRP K 353 HIS 0.009 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (18310) covalent geometry : angle 0.81578 / 0.45 (25948) hydrogen bonds : bond 0.05673 / 3.66 ( 821) hydrogen bonds : angle 4.59876 / 3.30 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7863 (m) cc_final: 0.7527 (p) REVERT: A 54 PHE cc_start: 0.8479 (m-80) cc_final: 0.8275 (m-10) REVERT: A 59 GLU cc_start: 0.8503 (pm20) cc_final: 0.8100 (pm20) REVERT: A 62 ILE cc_start: 0.8929 (mm) cc_final: 0.8604 (mt) REVERT: A 69 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.7874 (ttp-110) REVERT: A 74 ILE cc_start: 0.8715 (tp) cc_final: 0.8446 (tp) REVERT: A 97 GLU cc_start: 0.7728 (tp30) cc_final: 0.7411 (tp30) REVERT: A 125 LYS cc_start: 0.8675 (tppt) cc_final: 0.8237 (tppt) REVERT: A 129 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8202 (tpt-90) REVERT: B 37 LEU cc_start: 0.8982 (tp) cc_final: 0.8727 (tp) REVERT: B 39 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7884 (mmm-85) REVERT: B 88 TYR cc_start: 0.8831 (m-10) cc_final: 0.8398 (m-80) REVERT: C 30 ARG cc_start: 0.7352 (ptm160) cc_final: 0.7001 (mtp85) REVERT: C 44 ARG cc_start: 0.7136 (pmt170) cc_final: 0.6930 (pmt170) REVERT: C 63 GLU cc_start: 0.8161 (pp20) cc_final: 0.7795 (pp20) REVERT: D 37 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7374 (mtpp) REVERT: D 44 ILE cc_start: 0.8460 (pt) cc_final: 0.8206 (pt) REVERT: D 74 GLU cc_start: 0.7303 (tp30) cc_final: 0.7097 (tp30) REVERT: D 86 TYR cc_start: 0.8066 (m-10) cc_final: 0.6777 (m-10) REVERT: D 108 GLU cc_start: 0.7238 (pp20) cc_final: 0.6916 (pp20) REVERT: E 48 LEU cc_start: 0.8210 (mp) cc_final: 0.7737 (mp) REVERT: E 76 GLN cc_start: 0.7683 (tp40) cc_final: 0.7367 (tp40) REVERT: F 36 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.8035 (ttm-80) REVERT: F 45 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8061 (ttp-110) REVERT: F 61 PHE cc_start: 0.8653 (t80) cc_final: 0.8378 (t80) REVERT: F 88 TYR cc_start: 0.7484 (m-10) cc_final: 0.7078 (m-10) REVERT: G 44 ARG cc_start: 0.7270 (tpt90) cc_final: 0.6848 (tpt170) REVERT: G 56 VAL cc_start: 0.7966 (t) cc_final: 0.7673 (t) REVERT: G 66 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6671 (tm-30) REVERT: G 67 LEU cc_start: 0.8190 (mt) cc_final: 0.7766 (mt) REVERT: G 76 LYS cc_start: 0.7555 (tptp) cc_final: 0.7294 (tptp) REVERT: G 81 THR cc_start: 0.8480 (m) cc_final: 0.8217 (p) REVERT: G 87 LEU cc_start: 0.7180 (tp) cc_final: 0.6418 (tp) REVERT: H 74 GLU cc_start: 0.7742 (tp30) cc_final: 0.7522 (tp30) REVERT: H 118 THR cc_start: 0.8645 (t) cc_final: 0.8405 (p) REVERT: K 167 LEU cc_start: 0.8758 (mm) cc_final: 0.8412 (tp) REVERT: K 170 ILE cc_start: 0.8565 (mt) cc_final: 0.8145 (pt) REVERT: K 195 ILE cc_start: 0.6689 (tp) cc_final: 0.6432 (tp) REVERT: K 214 TYR cc_start: 0.8623 (t80) cc_final: 0.8398 (t80) REVERT: K 269 ASP cc_start: 0.8434 (m-30) cc_final: 0.8219 (m-30) REVERT: K 273 PHE cc_start: 0.7448 (m-10) cc_final: 0.7186 (m-10) REVERT: K 310 GLN cc_start: 0.6877 (pp30) cc_final: 0.6271 (pp30) REVERT: K 381 THR cc_start: 0.8945 (m) cc_final: 0.8539 (t) REVERT: K 406 ASN cc_start: 0.7688 (p0) cc_final: 0.7368 (p0) REVERT: L 40 GLU cc_start: 0.7877 (tp30) cc_final: 0.7587 (tp30) REVERT: M 209 MET cc_start: 0.6254 (ttp) cc_final: 0.5925 (ttp) REVERT: N 8 GLU cc_start: 0.8371 (mp0) cc_final: 0.8046 (mp0) REVERT: N 31 ASN cc_start: 0.7920 (m110) cc_final: 0.7590 (t0) REVERT: N 97 ILE cc_start: 0.7995 (mt) cc_final: 0.7790 (mt) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1828 time to fit residues: 131.9595 Evaluate side-chains 462 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN K 312 GLN K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084634 restraints weight = 59150.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.086651 restraints weight = 34735.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.087983 restraints weight = 23693.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088852 restraints weight = 18167.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089412 restraints weight = 15229.490| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 18310 Z= 0.302 Angle : 0.953 12.707 25948 Z= 0.518 Chirality : 0.057 0.619 2924 Planarity : 0.006 0.072 2268 Dihedral : 29.365 96.664 4818 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.15 % 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: -2.80 (0.21), residues: 1373 helix: -1.10 (0.18), residues: 713 sheet: -2.84 (1.04), residues: 26 loop : -2.73 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 78 TYR 0.024 0.003 TYR B 51 PHE 0.040 0.003 PHE K 236 TRP 0.048 0.004 TRP K 353 HIS 0.011 0.002 HIS K 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.30 (18310) covalent geometry : angle 0.95348 / 0.52 (25948) hydrogen bonds : bond 0.07518 / 4.87 ( 821) hydrogen bonds : angle 4.80573 / 3.43 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: A 57 SER cc_start: 0.8428 (t) cc_final: 0.7787 (p) REVERT: A 59 GLU cc_start: 0.8566 (pm20) cc_final: 0.7959 (pm20) REVERT: A 62 ILE cc_start: 0.8938 (mm) cc_final: 0.8672 (mp) REVERT: A 69 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8088 (ttp-110) REVERT: A 97 GLU cc_start: 0.7580 (tp30) cc_final: 0.6786 (tp30) REVERT: A 125 LYS cc_start: 0.8546 (tppt) cc_final: 0.8276 (tppt) REVERT: B 39 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7710 (mmt90) REVERT: B 59 LYS cc_start: 0.8970 (tppp) cc_final: 0.8652 (tppt) REVERT: B 88 TYR cc_start: 0.8766 (m-10) cc_final: 0.8386 (m-80) REVERT: C 63 GLU cc_start: 0.7966 (pp20) cc_final: 0.7748 (pp20) REVERT: D 37 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7628 (mtpp) REVERT: D 86 TYR cc_start: 0.8017 (m-10) cc_final: 0.6811 (m-10) REVERT: D 96 GLU cc_start: 0.7856 (mp0) cc_final: 0.7454 (mp0) REVERT: E 76 GLN cc_start: 0.7569 (tp40) cc_final: 0.7320 (tp40) REVERT: E 78 PHE cc_start: 0.8570 (m-10) cc_final: 0.8332 (m-10) REVERT: F 49 LEU cc_start: 0.8032 (tt) cc_final: 0.7700 (tp) REVERT: F 61 PHE cc_start: 0.8598 (t80) cc_final: 0.8303 (t80) REVERT: F 82 THR cc_start: 0.8851 (t) cc_final: 0.8622 (t) REVERT: F 88 TYR cc_start: 0.7613 (m-10) cc_final: 0.7040 (m-10) REVERT: G 30 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7237 (ttp-170) REVERT: G 66 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7124 (tm-30) REVERT: G 67 LEU cc_start: 0.8228 (mt) cc_final: 0.7794 (mt) REVERT: G 81 THR cc_start: 0.8475 (m) cc_final: 0.8258 (p) REVERT: G 87 LEU cc_start: 0.7176 (tp) cc_final: 0.6819 (tp) REVERT: G 113 ASN cc_start: 0.8960 (t0) cc_final: 0.8732 (t0) REVERT: H 59 GLN cc_start: 0.7708 (tp40) cc_final: 0.7505 (tp-100) REVERT: H 74 GLU cc_start: 0.7662 (tp30) cc_final: 0.7386 (tp30) REVERT: H 109 LEU cc_start: 0.8843 (pp) cc_final: 0.8607 (pt) REVERT: K 170 ILE cc_start: 0.8519 (mt) cc_final: 0.8310 (mm) REVERT: K 269 ASP cc_start: 0.8336 (m-30) cc_final: 0.8068 (m-30) REVERT: K 292 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7890 (mmmm) REVERT: K 310 GLN cc_start: 0.6926 (pp30) cc_final: 0.6508 (pp30) REVERT: K 350 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7608 (ttp-110) REVERT: K 406 ASN cc_start: 0.8171 (p0) cc_final: 0.7925 (p0) REVERT: L 40 GLU cc_start: 0.8118 (tp30) cc_final: 0.7730 (tp30) REVERT: M 209 MET cc_start: 0.6674 (ttp) cc_final: 0.6371 (ttp) REVERT: M 278 TYR cc_start: 0.5833 (t80) cc_final: 0.5510 (t80) REVERT: N 8 GLU cc_start: 0.8338 (mp0) cc_final: 0.8049 (mp0) REVERT: N 17 LEU cc_start: 0.7251 (mt) cc_final: 0.7035 (mt) REVERT: N 26 GLU cc_start: 0.7836 (tt0) cc_final: 0.7402 (tt0) REVERT: N 31 ASN cc_start: 0.8117 (m110) cc_final: 0.7700 (t0) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.1693 time to fit residues: 122.1178 Evaluate side-chains 466 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS E 108 ASN H 98 GLN K 301 ASN L 20 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086970 restraints weight = 58498.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089152 restraints weight = 33336.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090579 restraints weight = 22250.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091509 restraints weight = 16837.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092088 restraints weight = 13932.805| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18310 Z= 0.187 Angle : 0.819 11.518 25948 Z= 0.449 Chirality : 0.050 0.239 2924 Planarity : 0.005 0.066 2268 Dihedral : 29.329 92.555 4818 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.46 (0.21), residues: 1373 helix: -0.82 (0.18), residues: 710 sheet: -2.62 (1.03), residues: 26 loop : -2.58 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 78 TYR 0.034 0.002 TYR B 51 PHE 0.036 0.003 PHE K 236 TRP 0.026 0.003 TRP K 353 HIS 0.005 0.001 HIS M 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (18310) covalent geometry : angle 0.81891 / 0.45 (25948) hydrogen bonds : bond 0.05685 / 3.66 ( 821) hydrogen bonds : angle 4.56905 / 3.25 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7658 (m) cc_final: 0.7396 (p) REVERT: A 58 THR cc_start: 0.8736 (p) cc_final: 0.8386 (p) REVERT: A 59 GLU cc_start: 0.8497 (pm20) cc_final: 0.8117 (pm20) REVERT: A 69 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8313 (ttp-110) REVERT: A 97 GLU cc_start: 0.7591 (tp30) cc_final: 0.7306 (tp30) REVERT: A 125 LYS cc_start: 0.8591 (tppt) cc_final: 0.8275 (tppt) REVERT: B 53 GLU cc_start: 0.7765 (pp20) cc_final: 0.7515 (pp20) REVERT: B 59 LYS cc_start: 0.8958 (tppp) cc_final: 0.8618 (tppp) REVERT: C 63 GLU cc_start: 0.7834 (pp20) cc_final: 0.7622 (pp20) REVERT: D 37 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7608 (mtpp) REVERT: D 86 TYR cc_start: 0.8196 (m-10) cc_final: 0.6875 (m-10) REVERT: D 96 GLU cc_start: 0.7867 (mp0) cc_final: 0.7437 (mp0) REVERT: D 112 HIS cc_start: 0.8277 (m170) cc_final: 0.7454 (m-70) REVERT: E 58 THR cc_start: 0.9107 (p) cc_final: 0.8845 (p) REVERT: E 64 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8209 (mtpt) REVERT: E 74 ILE cc_start: 0.8909 (mm) cc_final: 0.8276 (tp) REVERT: E 76 GLN cc_start: 0.7481 (tp40) cc_final: 0.7279 (tp40) REVERT: E 95 SER cc_start: 0.8410 (p) cc_final: 0.8135 (t) REVERT: F 61 PHE cc_start: 0.8554 (t80) cc_final: 0.8283 (t80) REVERT: F 88 TYR cc_start: 0.7566 (m-10) cc_final: 0.6961 (m-10) REVERT: G 48 LYS cc_start: 0.7773 (mmpt) cc_final: 0.7448 (mmpt) REVERT: G 66 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7086 (tm-30) REVERT: G 67 LEU cc_start: 0.8270 (mt) cc_final: 0.7885 (mt) REVERT: G 87 LEU cc_start: 0.7152 (tp) cc_final: 0.6581 (tp) REVERT: H 38 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7919 (tm-30) REVERT: K 253 LEU cc_start: 0.8195 (mt) cc_final: 0.7883 (mt) REVERT: K 353 TRP cc_start: 0.8455 (m-90) cc_final: 0.8033 (m-90) REVERT: K 364 HIS cc_start: 0.7467 (t70) cc_final: 0.7203 (t70) REVERT: K 372 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7586 (tp30) REVERT: K 406 ASN cc_start: 0.7999 (p0) cc_final: 0.7739 (p0) REVERT: L 40 GLU cc_start: 0.8068 (tp30) cc_final: 0.7705 (tp30) REVERT: M 209 MET cc_start: 0.6399 (ttp) cc_final: 0.6061 (ttp) REVERT: N 8 GLU cc_start: 0.8339 (mp0) cc_final: 0.8042 (mp0) REVERT: N 26 GLU cc_start: 0.7774 (tt0) cc_final: 0.7511 (tt0) REVERT: N 31 ASN cc_start: 0.8017 (m110) cc_final: 0.7631 (t0) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1697 time to fit residues: 123.3740 Evaluate side-chains 479 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 80 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 140 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS C 86 GLN G 38 HIS H 50 GLN H 98 GLN ** K 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.104924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.087908 restraints weight = 59185.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090077 restraints weight = 33694.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.091476 restraints weight = 22559.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092420 restraints weight = 17065.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092966 restraints weight = 14155.214| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18310 Z= 0.171 Angle : 0.820 11.797 25948 Z= 0.449 Chirality : 0.049 0.380 2924 Planarity : 0.005 0.067 2268 Dihedral : 29.245 87.591 4818 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.39 (0.21), residues: 1373 helix: -0.80 (0.18), residues: 716 sheet: -2.49 (1.04), residues: 26 loop : -2.50 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 36 TYR 0.023 0.002 TYR B 51 PHE 0.038 0.002 PHE N 21 TRP 0.024 0.002 TRP K 353 HIS 0.010 0.001 HIS K 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (18310) covalent geometry : angle 0.81954 / 0.45 (25948) hydrogen bonds : bond 0.05305 / 3.42 ( 821) hydrogen bonds : angle 4.52354 / 3.24 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7580 (m) cc_final: 0.7310 (p) REVERT: A 49 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7258 (mtp180) REVERT: A 58 THR cc_start: 0.8683 (p) cc_final: 0.8351 (p) REVERT: A 59 GLU cc_start: 0.8481 (pm20) cc_final: 0.8083 (pm20) REVERT: A 69 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8323 (ttp-110) REVERT: A 97 GLU cc_start: 0.7586 (tp30) cc_final: 0.6982 (mm-30) REVERT: A 106 ASP cc_start: 0.7321 (m-30) cc_final: 0.7115 (m-30) REVERT: A 125 LYS cc_start: 0.8567 (tppt) cc_final: 0.8270 (tppt) REVERT: A 128 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: B 37 LEU cc_start: 0.8888 (tp) cc_final: 0.8568 (tp) REVERT: B 52 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 55 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8252 (mtt180) REVERT: B 59 LYS cc_start: 0.8912 (tppp) cc_final: 0.8707 (tppp) REVERT: B 88 TYR cc_start: 0.7981 (m-80) cc_final: 0.7411 (m-80) REVERT: D 37 LYS cc_start: 0.8491 (mtmm) cc_final: 0.7671 (mtpp) REVERT: D 86 TYR cc_start: 0.7654 (m-10) cc_final: 0.6679 (m-10) REVERT: D 96 GLU cc_start: 0.7825 (mp0) cc_final: 0.7464 (mp0) REVERT: D 108 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6088 (tp30) REVERT: D 112 HIS cc_start: 0.8124 (m170) cc_final: 0.7589 (m-70) REVERT: E 58 THR cc_start: 0.9101 (p) cc_final: 0.8873 (p) REVERT: E 73 GLU cc_start: 0.7624 (pt0) cc_final: 0.6440 (pt0) REVERT: E 76 GLN cc_start: 0.7547 (tp40) cc_final: 0.7312 (tp40) REVERT: E 95 SER cc_start: 0.8399 (p) cc_final: 0.8133 (t) REVERT: E 125 LYS cc_start: 0.8165 (ptpp) cc_final: 0.7686 (pttp) REVERT: F 27 GLN cc_start: 0.7977 (mp10) cc_final: 0.7546 (mp10) REVERT: F 36 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7763 (ttm110) REVERT: F 49 LEU cc_start: 0.8194 (tt) cc_final: 0.7765 (tt) REVERT: F 61 PHE cc_start: 0.8669 (t80) cc_final: 0.8389 (t80) REVERT: F 88 TYR cc_start: 0.7553 (m-10) cc_final: 0.7003 (m-10) REVERT: G 67 LEU cc_start: 0.8268 (mt) cc_final: 0.7903 (mt) REVERT: G 87 LEU cc_start: 0.7125 (tp) cc_final: 0.6570 (tp) REVERT: K 167 LEU cc_start: 0.8673 (mm) cc_final: 0.8304 (mm) REVERT: K 250 ASN cc_start: 0.7601 (p0) cc_final: 0.7264 (p0) REVERT: K 353 TRP cc_start: 0.8417 (m-90) cc_final: 0.8211 (m-90) REVERT: K 357 LEU cc_start: 0.8352 (mt) cc_final: 0.8126 (mt) REVERT: K 364 HIS cc_start: 0.7274 (t70) cc_final: 0.6992 (t70) REVERT: K 372 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7478 (tm-30) REVERT: L 40 GLU cc_start: 0.8025 (tp30) cc_final: 0.7621 (tp30) REVERT: M 209 MET cc_start: 0.6337 (ttp) cc_final: 0.5952 (ttp) REVERT: M 234 LEU cc_start: 0.7003 (mt) cc_final: 0.6802 (mt) REVERT: M 280 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7887 (mpt-90) REVERT: N 8 GLU cc_start: 0.8354 (mp0) cc_final: 0.8039 (mp0) REVERT: N 31 ASN cc_start: 0.8034 (m110) cc_final: 0.7630 (t0) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.1594 time to fit residues: 114.6275 Evaluate side-chains 479 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 144 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 68 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS H 98 GLN K 285 HIS ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.105703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088700 restraints weight = 59309.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090890 restraints weight = 33858.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092327 restraints weight = 22648.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093254 restraints weight = 17101.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.093834 restraints weight = 14167.741| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18310 Z= 0.171 Angle : 0.810 12.005 25948 Z= 0.443 Chirality : 0.048 0.246 2924 Planarity : 0.006 0.065 2268 Dihedral : 29.170 87.090 4818 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.29 (0.22), residues: 1373 helix: -0.71 (0.19), residues: 719 sheet: -2.51 (0.97), residues: 26 loop : -2.46 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 78 TYR 0.029 0.002 TYR K 214 PHE 0.032 0.003 PHE A 104 TRP 0.022 0.003 TRP K 353 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (18310) covalent geometry : angle 0.81030 / 0.44 (25948) hydrogen bonds : bond 0.05155 / 3.34 ( 821) hydrogen bonds : angle 4.49108 / 3.22 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8698 (p) cc_final: 0.8173 (t) REVERT: A 59 GLU cc_start: 0.8434 (pm20) cc_final: 0.8007 (pm20) REVERT: A 69 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8234 (ttp-110) REVERT: A 97 GLU cc_start: 0.7530 (tp30) cc_final: 0.6812 (mm-30) REVERT: A 125 LYS cc_start: 0.8471 (tppt) cc_final: 0.8189 (tppt) REVERT: B 37 LEU cc_start: 0.8733 (tp) cc_final: 0.8292 (tp) REVERT: B 88 TYR cc_start: 0.7884 (m-80) cc_final: 0.7326 (m-80) REVERT: C 52 TYR cc_start: 0.6438 (p90) cc_final: 0.6228 (p90) REVERT: D 37 LYS cc_start: 0.8535 (mtmm) cc_final: 0.7720 (mtpp) REVERT: D 86 TYR cc_start: 0.7711 (m-10) cc_final: 0.7139 (m-10) REVERT: D 96 GLU cc_start: 0.7896 (mp0) cc_final: 0.7521 (mp0) REVERT: D 102 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7785 (ttm110) REVERT: E 64 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7772 (mtpt) REVERT: E 76 GLN cc_start: 0.7502 (tp40) cc_final: 0.7282 (tp40) REVERT: E 125 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7832 (pttp) REVERT: F 82 THR cc_start: 0.8838 (t) cc_final: 0.8623 (t) REVERT: F 88 TYR cc_start: 0.7505 (m-10) cc_final: 0.7004 (m-10) REVERT: G 31 ILE cc_start: 0.8828 (tt) cc_final: 0.8568 (tt) REVERT: G 66 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6604 (tm-30) REVERT: G 67 LEU cc_start: 0.8259 (mt) cc_final: 0.7933 (mt) REVERT: G 87 LEU cc_start: 0.6873 (tp) cc_final: 0.6430 (tp) REVERT: K 176 GLU cc_start: 0.8048 (tp30) cc_final: 0.7442 (tm-30) REVERT: K 245 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7450 (tmm160) REVERT: K 251 LEU cc_start: 0.8227 (mm) cc_final: 0.7957 (mm) REVERT: K 253 LEU cc_start: 0.8094 (mt) cc_final: 0.7838 (mt) REVERT: K 292 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7475 (mmmt) REVERT: K 331 GLU cc_start: 0.7191 (pm20) cc_final: 0.6921 (pm20) REVERT: K 353 TRP cc_start: 0.8426 (m-90) cc_final: 0.8181 (m-90) REVERT: K 364 HIS cc_start: 0.7106 (t70) cc_final: 0.6879 (t70) REVERT: K 372 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7435 (tm-30) REVERT: L 40 GLU cc_start: 0.7901 (tp30) cc_final: 0.7582 (tp30) REVERT: M 209 MET cc_start: 0.6349 (ttp) cc_final: 0.5955 (ttp) REVERT: M 280 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7870 (mpt-90) REVERT: N 7 LEU cc_start: 0.8295 (pp) cc_final: 0.8012 (pp) REVERT: N 8 GLU cc_start: 0.8309 (mp0) cc_final: 0.7823 (mp0) REVERT: N 31 ASN cc_start: 0.8015 (m110) cc_final: 0.7601 (t0) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.1677 time to fit residues: 119.7898 Evaluate side-chains 464 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 38 HIS H 98 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.104830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088132 restraints weight = 59122.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090119 restraints weight = 35091.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091442 restraints weight = 24213.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092279 restraints weight = 18739.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092792 restraints weight = 15811.968| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 18310 Z= 0.197 Angle : 0.846 21.210 25948 Z= 0.460 Chirality : 0.049 0.217 2924 Planarity : 0.007 0.149 2268 Dihedral : 29.127 87.641 4818 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.38 (0.21), residues: 1373 helix: -0.82 (0.18), residues: 723 sheet: -2.58 (0.99), residues: 26 loop : -2.46 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG E 63 TYR 0.037 0.003 TYR K 352 PHE 0.048 0.002 PHE N 21 TRP 0.030 0.003 TRP K 353 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (18310) covalent geometry : angle 0.84624 / 0.46 (25948) hydrogen bonds : bond 0.05502 / 3.55 ( 821) hydrogen bonds : angle 4.52319 / 3.23 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8589 (m-80) cc_final: 0.8383 (m-80) REVERT: A 58 THR cc_start: 0.8809 (p) cc_final: 0.8246 (t) REVERT: A 59 GLU cc_start: 0.8441 (pm20) cc_final: 0.8037 (pm20) REVERT: A 69 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8180 (ttp-110) REVERT: A 97 GLU cc_start: 0.7491 (tp30) cc_final: 0.6736 (mm-30) REVERT: A 125 LYS cc_start: 0.8453 (tppt) cc_final: 0.8192 (tppt) REVERT: B 37 LEU cc_start: 0.8743 (tp) cc_final: 0.8345 (tp) REVERT: B 39 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: B 52 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 53 GLU cc_start: 0.7609 (pp20) cc_final: 0.7270 (pp20) REVERT: B 88 TYR cc_start: 0.7902 (m-80) cc_final: 0.7453 (m-80) REVERT: C 31 ILE cc_start: 0.8721 (mm) cc_final: 0.7944 (mm) REVERT: D 37 LYS cc_start: 0.8542 (mtmm) cc_final: 0.7803 (mtpp) REVERT: D 72 ILE cc_start: 0.8606 (tt) cc_final: 0.7988 (tt) REVERT: D 86 TYR cc_start: 0.7784 (m-10) cc_final: 0.7055 (m-10) REVERT: D 96 GLU cc_start: 0.7815 (mp0) cc_final: 0.7541 (mp0) REVERT: D 98 GLN cc_start: 0.7699 (tp40) cc_final: 0.7388 (tp40) REVERT: D 102 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7689 (ttm110) REVERT: E 73 GLU cc_start: 0.6447 (mt-10) cc_final: 0.4837 (mt-10) REVERT: E 76 GLN cc_start: 0.7538 (tp40) cc_final: 0.7254 (tp40) REVERT: E 95 SER cc_start: 0.8439 (p) cc_final: 0.8158 (t) REVERT: E 125 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7874 (pttp) REVERT: F 82 THR cc_start: 0.8794 (t) cc_final: 0.8577 (t) REVERT: F 88 TYR cc_start: 0.7642 (m-10) cc_final: 0.7102 (m-10) REVERT: G 30 ARG cc_start: 0.7200 (ttp-170) cc_final: 0.6985 (ttm170) REVERT: G 44 ARG cc_start: 0.6853 (tpt90) cc_final: 0.6524 (tpt170) REVERT: G 56 VAL cc_start: 0.7899 (t) cc_final: 0.7476 (t) REVERT: G 66 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6537 (tm-30) REVERT: G 67 LEU cc_start: 0.8297 (mt) cc_final: 0.7926 (mt) REVERT: G 87 LEU cc_start: 0.6903 (tp) cc_final: 0.6399 (tp) REVERT: H 74 GLU cc_start: 0.7537 (tp30) cc_final: 0.7319 (tp30) REVERT: K 176 GLU cc_start: 0.8063 (tp30) cc_final: 0.7590 (tm-30) REVERT: K 253 LEU cc_start: 0.8148 (mt) cc_final: 0.7901 (mt) REVERT: K 292 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7391 (mmmt) REVERT: K 331 GLU cc_start: 0.7579 (pm20) cc_final: 0.6960 (pm20) REVERT: K 343 ASP cc_start: 0.6393 (p0) cc_final: 0.6160 (p0) REVERT: K 364 HIS cc_start: 0.7305 (t70) cc_final: 0.7104 (t70) REVERT: L 40 GLU cc_start: 0.7869 (tp30) cc_final: 0.7520 (tp30) REVERT: M 209 MET cc_start: 0.6344 (ttp) cc_final: 0.5958 (ttp) REVERT: M 280 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7917 (mpt-90) REVERT: M 350 LEU cc_start: 0.9162 (tp) cc_final: 0.8958 (tp) REVERT: N 7 LEU cc_start: 0.8317 (pp) cc_final: 0.8016 (pp) REVERT: N 8 GLU cc_start: 0.8344 (mp0) cc_final: 0.7793 (mp0) REVERT: N 23 TYR cc_start: 0.7820 (t80) cc_final: 0.7393 (t80) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.1652 time to fit residues: 116.0317 Evaluate side-chains 460 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 44 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 156 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS E 108 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS H 98 GLN K 285 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089485 restraints weight = 59794.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.091718 restraints weight = 34059.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093162 restraints weight = 22693.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094095 restraints weight = 17086.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094690 restraints weight = 14119.083| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18310 Z= 0.166 Angle : 0.810 11.681 25948 Z= 0.442 Chirality : 0.047 0.211 2924 Planarity : 0.007 0.149 2268 Dihedral : 29.056 88.523 4818 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.31 (0.21), residues: 1373 helix: -0.76 (0.18), residues: 716 sheet: -2.62 (0.91), residues: 26 loop : -2.42 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 79 TYR 0.037 0.003 TYR G 59 PHE 0.043 0.002 PHE N 21 TRP 0.028 0.003 TRP K 353 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (18310) covalent geometry : angle 0.81038 / 0.44 (25948) hydrogen bonds : bond 0.05022 / 3.26 ( 821) hydrogen bonds : angle 4.52315 / 3.23 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.17 seconds wall clock time: 60 minutes 34.47 seconds (3634.47 seconds total)