Starting phenix.real_space_refine on Sat Jul 4 14:53:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2y_38022/07_2026/8x2y_38022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2y_38022/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x2y_38022/07_2026/8x2y_38022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2y_38022/07_2026/8x2y_38022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x2y_38022/07_2026/8x2y_38022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2y_38022/07_2026/8x2y_38022.map" } 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-dev-6108/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: 3.54, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 878.6 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: 2.09 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: 3.89 Time building geometry restraints manager: 1.95 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: 23823 1.92 - 3.84: 1894 3.84 - 5.76: 164 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.640 Find NCS groups from input model: 0.190 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- 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 : 1.079 9.607 25948 Z= 0.805 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 1.07934 / 0.80 (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 : 0.504 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 46 VAL cc_start: 0.8159 (p) cc_final: 0.7953 (p) REVERT: A 51 ILE cc_start: 0.7838 (mm) cc_final: 0.6978 (mm) REVERT: A 59 GLU cc_start: 0.8075 (pm20) cc_final: 0.7853 (pm20) REVERT: A 125 LYS cc_start: 0.8409 (tppt) cc_final: 0.7902 (tppt) REVERT: B 46 ILE cc_start: 0.7029 (mm) cc_final: 0.6718 (mm) REVERT: B 74 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7170 (tm-30) REVERT: D 57 ILE cc_start: 0.7453 (mm) cc_final: 0.6803 (mm) REVERT: D 74 GLU cc_start: 0.7390 (tp30) cc_final: 0.6795 (tp30) REVERT: D 104 ILE cc_start: 0.7634 (tp) cc_final: 0.7253 (tp) REVERT: E 46 VAL cc_start: 0.7293 (p) cc_final: 0.7029 (m) REVERT: E 62 ILE cc_start: 0.6465 (tt) cc_final: 0.5903 (tp) REVERT: E 78 PHE cc_start: 0.8033 (m-10) cc_final: 0.6286 (m-10) REVERT: E 83 ARG cc_start: 0.7128 (tpm170) cc_final: 0.6622 (mmm160) REVERT: F 82 THR cc_start: 0.7623 (t) cc_final: 0.6856 (p) REVERT: G 24 LEU cc_start: 0.8512 (mt) cc_final: 0.7914 (mt) REVERT: G 67 LEU cc_start: 0.7687 (mt) cc_final: 0.6916 (mt) REVERT: H 63 SER cc_start: 0.8015 (t) cc_final: 0.7546 (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: 0.8238 (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: 0.8011 (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: 0.5511 (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: 0.6778 (mt0) REVERT: K 350 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7526 (mtt90) REVERT: K 364 HIS cc_start: 0.6767 (t-90) cc_final: 0.6402 (t-90) REVERT: K 372 GLU cc_start: 0.8469 (tt0) cc_final: 0.8008 (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: 0.3551 (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: 0.7945 (tp) REVERT: M 278 TYR cc_start: 0.6380 (t80) cc_final: 0.6140 (t80) REVERT: N 23 TYR cc_start: 0.7272 (t80) cc_final: 0.7040 (t80) REVERT: N 97 ILE cc_start: 0.7171 (mt) cc_final: 0.6956 (mt) outliers start: 10 outliers final: 1 residues processed: 557 average time/residue: 0.1770 time to fit residues: 136.7763 Evaluate side-chains 438 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 0.9980 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 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.106213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089301 restraints weight = 58043.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091794 restraints weight = 30621.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093410 restraints weight = 19280.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094449 restraints weight = 13797.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095170 restraints weight = 11019.946| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18310 Z= 0.191 Angle : 0.848 10.774 25948 Z= 0.470 Chirality : 0.050 0.222 2924 Planarity : 0.006 0.060 2268 Dihedral : 29.795 89.893 4818 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.64 % Allowed : 6.26 % Favored : 93.10 % 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: -3.41 (0.20), residues: 1373 helix: -1.93 (0.17), residues: 688 sheet: -2.15 (0.96), residues: 26 loop : -2.62 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 39 TYR 0.031 0.002 TYR F 98 PHE 0.024 0.002 PHE E 54 TRP 0.019 0.002 TRP K 247 HIS 0.011 0.002 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (18310) covalent geometry : angle 0.84836 / 0.47 (25948) hydrogen bonds : bond 0.06058 / 3.98 ( 821) hydrogen bonds : angle 5.19541 / 3.72 ( 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 490 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 482 time to evaluate : 0.631 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: A 46 VAL cc_start: 0.8394 (p) cc_final: 0.7492 (p) REVERT: A 50 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: A 51 ILE cc_start: 0.8233 (mm) cc_final: 0.7876 (mm) REVERT: A 125 LYS cc_start: 0.8425 (tppt) cc_final: 0.7953 (tppt) REVERT: B 37 LEU cc_start: 0.8809 (tp) cc_final: 0.8302 (tp) REVERT: B 39 ARG cc_start: 0.7248 (tpp80) cc_final: 0.6493 (mmt90) REVERT: B 78 ARG cc_start: 0.7113 (ttp-110) cc_final: 0.6868 (ttp-110) REVERT: C 18 SER cc_start: 0.8101 (p) cc_final: 0.7463 (t) REVERT: C 74 ASP cc_start: 0.7638 (t0) cc_final: 0.7309 (t0) REVERT: D 57 ILE cc_start: 0.7257 (mm) cc_final: 0.6887 (tp) REVERT: D 68 PHE cc_start: 0.7715 (t80) cc_final: 0.7104 (t80) REVERT: D 74 GLU cc_start: 0.7233 (tp30) cc_final: 0.7005 (tp30) REVERT: D 98 GLN cc_start: 0.7794 (tp40) cc_final: 0.7299 (tp40) REVERT: D 102 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7438 (ttm110) REVERT: E 83 ARG cc_start: 0.7067 (tpm170) cc_final: 0.6833 (mmm160) REVERT: F 27 GLN cc_start: 0.7461 (mp-120) cc_final: 0.5605 (mp10) REVERT: F 60 SER cc_start: 0.8371 (m) cc_final: 0.8112 (p) REVERT: F 63 GLU cc_start: 0.6606 (tp30) cc_final: 0.5841 (tp30) REVERT: F 78 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7323 (ptp90) REVERT: F 82 THR cc_start: 0.7819 (t) cc_final: 0.6794 (p) REVERT: H 63 SER cc_start: 0.8035 (t) cc_final: 0.7565 (p) REVERT: H 74 GLU cc_start: 0.7590 (tp30) cc_final: 0.7180 (tp30) REVERT: K 167 LEU cc_start: 0.8592 (mm) cc_final: 0.8116 (tp) REVERT: K 238 GLU cc_start: 0.6716 (tt0) cc_final: 0.5154 (mt-10) REVERT: K 250 ASN cc_start: 0.7371 (p0) cc_final: 0.6908 (p0) REVERT: K 269 ASP cc_start: 0.8629 (m-30) cc_final: 0.8350 (m-30) REVERT: K 274 TYR cc_start: 0.7172 (m-10) cc_final: 0.6505 (m-10) REVERT: K 275 CYS cc_start: 0.7098 (m) cc_final: 0.6868 (t) REVERT: K 357 LEU cc_start: 0.7525 (tp) cc_final: 0.7252 (tp) REVERT: K 364 HIS cc_start: 0.6692 (t-90) cc_final: 0.6366 (t-90) REVERT: M 141 PHE cc_start: 0.7865 (p90) cc_final: 0.7626 (p90) REVERT: N 31 ASN cc_start: 0.8306 (m110) cc_final: 0.7684 (t0) outliers start: 8 outliers final: 1 residues processed: 487 average time/residue: 0.1676 time to fit residues: 114.4758 Evaluate side-chains 431 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 0.3980 chunk 148 optimal weight: 7.9990 chunk 103 optimal weight: 0.0370 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 86 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 N 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089573 restraints weight = 58752.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092052 restraints weight = 31348.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093653 restraints weight = 19776.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094624 restraints weight = 14210.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095356 restraints weight = 11413.447| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18310 Z= 0.172 Angle : 0.763 10.139 25948 Z= 0.434 Chirality : 0.048 0.217 2924 Planarity : 0.005 0.072 2268 Dihedral : 29.583 90.129 4818 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.32 % Allowed : 5.46 % Favored : 94.22 % 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: -2.95 (0.20), residues: 1373 helix: -1.45 (0.18), residues: 693 sheet: -1.95 (1.08), residues: 26 loop : -2.52 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 39 TYR 0.027 0.002 TYR F 98 PHE 0.016 0.002 PHE K 236 TRP 0.043 0.003 TRP K 353 HIS 0.008 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (18310) covalent geometry : angle 0.76345 / 0.43 (25948) hydrogen bonds : bond 0.05686 / 3.70 ( 821) hydrogen bonds : angle 4.79599 / 3.47 ( 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 500 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 496 time to evaluate : 0.517 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: A 67 PHE cc_start: 0.7270 (t80) cc_final: 0.6903 (t80) REVERT: A 97 GLU cc_start: 0.7599 (tp30) cc_final: 0.7346 (tp30) REVERT: A 125 LYS cc_start: 0.8388 (tppt) cc_final: 0.7940 (tppt) REVERT: B 37 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 39 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6957 (mmt90) REVERT: B 78 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6831 (ttp-110) REVERT: C 74 ASP cc_start: 0.7752 (t0) cc_final: 0.7396 (t0) REVERT: D 42 SER cc_start: 0.8571 (m) cc_final: 0.8146 (p) REVERT: D 71 ASP cc_start: 0.7477 (p0) cc_final: 0.7243 (p0) REVERT: D 86 TYR cc_start: 0.8392 (m-10) cc_final: 0.7989 (m-10) REVERT: D 96 GLU cc_start: 0.7349 (mp0) cc_final: 0.6797 (mp0) REVERT: D 98 GLN cc_start: 0.7915 (tp40) cc_final: 0.7228 (tp40) REVERT: E 78 PHE cc_start: 0.7925 (m-10) cc_final: 0.7444 (m-10) REVERT: F 49 LEU cc_start: 0.6829 (tp) cc_final: 0.6404 (tp) REVERT: F 53 GLU cc_start: 0.7596 (mp0) cc_final: 0.7128 (mp0) REVERT: F 63 GLU cc_start: 0.6976 (tp30) cc_final: 0.6459 (tp30) REVERT: F 78 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7506 (ptp90) REVERT: F 82 THR cc_start: 0.8040 (t) cc_final: 0.7159 (p) REVERT: G 56 VAL cc_start: 0.8249 (t) cc_final: 0.8042 (m) REVERT: G 57 LEU cc_start: 0.8355 (tp) cc_final: 0.8139 (tp) REVERT: G 81 THR cc_start: 0.8070 (m) cc_final: 0.7557 (p) REVERT: H 74 GLU cc_start: 0.7568 (tp30) cc_final: 0.7216 (tp30) REVERT: K 167 LEU cc_start: 0.8543 (mm) cc_final: 0.8125 (tp) REVERT: K 238 GLU cc_start: 0.6592 (tt0) cc_final: 0.5705 (mt-10) REVERT: K 251 LEU cc_start: 0.7882 (mt) cc_final: 0.7587 (mp) REVERT: K 364 HIS cc_start: 0.6914 (t-90) cc_final: 0.6488 (t-90) REVERT: L 40 GLU cc_start: 0.7566 (tp30) cc_final: 0.6992 (tp30) REVERT: L 44 PHE cc_start: 0.7688 (m-10) cc_final: 0.7208 (m-10) REVERT: M 141 PHE cc_start: 0.7888 (p90) cc_final: 0.7679 (p90) REVERT: M 234 LEU cc_start: 0.6777 (mt) cc_final: 0.6524 (mt) REVERT: N 31 ASN cc_start: 0.8313 (m110) cc_final: 0.7820 (t0) REVERT: N 97 ILE cc_start: 0.7698 (mt) cc_final: 0.7447 (mt) outliers start: 4 outliers final: 1 residues processed: 497 average time/residue: 0.1651 time to fit residues: 114.9146 Evaluate side-chains 442 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 440 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 60 optimal weight: 0.0370 chunk 147 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 112 HIS E 39 HIS H 98 GLN K 285 HIS K 312 GLN ** L 25 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 = 0.3792 r_free = 0.3792 target = 0.105666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089148 restraints weight = 58433.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091545 restraints weight = 31000.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093076 restraints weight = 19539.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094103 restraints weight = 14040.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094749 restraints weight = 11195.253| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4193 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= 0.183 Angle : 0.785 10.760 25948 Z= 0.435 Chirality : 0.048 0.240 2924 Planarity : 0.006 0.098 2268 Dihedral : 29.445 96.550 4818 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % 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: -2.59 (0.21), residues: 1373 helix: -1.03 (0.19), residues: 692 sheet: -2.44 (1.02), residues: 26 loop : -2.46 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 169 TYR 0.024 0.002 TYR K 211 PHE 0.036 0.002 PHE A 104 TRP 0.018 0.001 TRP K 353 HIS 0.006 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (18310) covalent geometry : angle 0.78492 / 0.43 (25948) hydrogen bonds : bond 0.05454 / 3.55 ( 821) hydrogen bonds : angle 4.61256 / 3.31 ( 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 494 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 0.502 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 125 LYS cc_start: 0.8468 (tppt) cc_final: 0.7964 (tppt) REVERT: C 63 GLU cc_start: 0.8067 (pp20) cc_final: 0.7640 (tm-30) REVERT: C 74 ASP cc_start: 0.7855 (t0) cc_final: 0.7650 (t0) REVERT: D 38 GLU cc_start: 0.6958 (tp30) cc_final: 0.6717 (tp30) REVERT: D 42 SER cc_start: 0.8591 (m) cc_final: 0.8216 (p) REVERT: D 74 GLU cc_start: 0.7231 (tp30) cc_final: 0.6565 (tp30) REVERT: D 89 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7559 (mmmt) REVERT: D 96 GLU cc_start: 0.7488 (mp0) cc_final: 0.7011 (mp0) REVERT: E 65 LEU cc_start: 0.8099 (tt) cc_final: 0.7896 (tp) REVERT: E 83 ARG cc_start: 0.7228 (tpm170) cc_final: 0.6858 (mmm160) REVERT: F 27 GLN cc_start: 0.7764 (mp10) cc_final: 0.7274 (mp10) REVERT: F 49 LEU cc_start: 0.7398 (tp) cc_final: 0.6905 (tp) REVERT: F 63 GLU cc_start: 0.7107 (tp30) cc_final: 0.6896 (tp30) REVERT: F 78 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7636 (ptp90) REVERT: F 82 THR cc_start: 0.8162 (t) cc_final: 0.7246 (p) REVERT: F 88 TYR cc_start: 0.6786 (m-10) cc_final: 0.6416 (m-10) REVERT: G 56 VAL cc_start: 0.8161 (t) cc_final: 0.7894 (m) REVERT: G 67 LEU cc_start: 0.8051 (mt) cc_final: 0.7560 (mt) REVERT: G 81 THR cc_start: 0.8319 (m) cc_final: 0.7820 (p) REVERT: H 50 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7588 (tm-30) REVERT: H 74 GLU cc_start: 0.7670 (tp30) cc_final: 0.7261 (tp30) REVERT: K 167 LEU cc_start: 0.8625 (mm) cc_final: 0.8127 (tp) REVERT: K 170 ILE cc_start: 0.8732 (mt) cc_final: 0.8146 (mt) REVERT: K 238 GLU cc_start: 0.6819 (tt0) cc_final: 0.5768 (mt-10) REVERT: K 251 LEU cc_start: 0.8068 (mt) cc_final: 0.7749 (mt) REVERT: K 287 VAL cc_start: 0.8004 (p) cc_final: 0.7310 (p) REVERT: K 364 HIS cc_start: 0.7026 (t-90) cc_final: 0.6631 (t-90) REVERT: K 406 ASN cc_start: 0.5991 (p0) cc_final: 0.5753 (p0) REVERT: L 40 GLU cc_start: 0.7526 (tp30) cc_final: 0.6866 (tp30) REVERT: L 44 PHE cc_start: 0.7657 (m-10) cc_final: 0.7068 (m-10) REVERT: N 8 GLU cc_start: 0.8310 (mp0) cc_final: 0.8007 (mp0) REVERT: N 31 ASN cc_start: 0.8155 (m110) cc_final: 0.7753 (t0) REVERT: N 96 LEU cc_start: 0.8401 (pp) cc_final: 0.8049 (pp) REVERT: N 97 ILE cc_start: 0.7860 (mt) cc_final: 0.7646 (mt) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.1668 time to fit residues: 114.9417 Evaluate side-chains 455 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 112 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 GLN K 401 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 = 0.3783 r_free = 0.3783 target = 0.105259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088389 restraints weight = 58008.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090793 restraints weight = 31028.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092336 restraints weight = 19658.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093337 restraints weight = 14223.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093935 restraints weight = 11455.003| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18310 Z= 0.192 Angle : 0.774 11.362 25948 Z= 0.431 Chirality : 0.048 0.217 2924 Planarity : 0.005 0.081 2268 Dihedral : 29.340 91.214 4818 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -2.56 (0.21), residues: 1373 helix: -0.98 (0.18), residues: 695 sheet: -2.21 (1.06), residues: 26 loop : -2.51 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 116 TYR 0.018 0.002 TYR D 43 PHE 0.029 0.002 PHE K 236 TRP 0.052 0.003 TRP K 353 HIS 0.006 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (18310) covalent geometry : angle 0.77353 / 0.43 (25948) hydrogen bonds : bond 0.05584 / 3.62 ( 821) hydrogen bonds : angle 4.55300 / 3.29 ( 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 498 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.390 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: A 125 LYS cc_start: 0.8605 (tppt) cc_final: 0.8128 (tppt) REVERT: B 67 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: C 84 HIS cc_start: 0.6951 (t-170) cc_final: 0.6748 (t-170) REVERT: D 42 SER cc_start: 0.8589 (m) cc_final: 0.8311 (p) REVERT: D 57 ILE cc_start: 0.8100 (mm) cc_final: 0.7747 (tp) REVERT: D 71 ASP cc_start: 0.7436 (p0) cc_final: 0.6424 (p0) REVERT: D 86 TYR cc_start: 0.8193 (m-10) cc_final: 0.6877 (m-10) REVERT: D 96 GLU cc_start: 0.7580 (mp0) cc_final: 0.7005 (mp0) REVERT: E 45 THR cc_start: 0.7367 (p) cc_final: 0.7086 (p) REVERT: E 48 LEU cc_start: 0.8162 (mt) cc_final: 0.7877 (mp) REVERT: E 60 LEU cc_start: 0.8933 (pp) cc_final: 0.8255 (pp) REVERT: E 73 GLU cc_start: 0.6967 (mp0) cc_final: 0.6509 (mp0) REVERT: E 125 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7567 (mtmm) REVERT: F 82 THR cc_start: 0.8431 (t) cc_final: 0.7574 (p) REVERT: F 88 TYR cc_start: 0.7082 (m-10) cc_final: 0.6618 (m-10) REVERT: G 67 LEU cc_start: 0.8102 (mt) cc_final: 0.7765 (mt) REVERT: G 81 THR cc_start: 0.8346 (m) cc_final: 0.7845 (p) REVERT: G 87 LEU cc_start: 0.7936 (tt) cc_final: 0.7411 (tt) REVERT: G 94 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7332 (mm-30) REVERT: H 50 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 65 LEU cc_start: 0.8073 (mm) cc_final: 0.7850 (mm) REVERT: H 74 GLU cc_start: 0.7678 (tp30) cc_final: 0.7288 (tp30) REVERT: K 238 GLU cc_start: 0.6839 (tt0) cc_final: 0.6073 (mt-10) REVERT: K 251 LEU cc_start: 0.8118 (mt) cc_final: 0.7641 (mp) REVERT: K 269 ASP cc_start: 0.8501 (m-30) cc_final: 0.8299 (m-30) REVERT: K 349 TYR cc_start: 0.6451 (m-80) cc_final: 0.5987 (m-80) REVERT: L 40 GLU cc_start: 0.7636 (tp30) cc_final: 0.6983 (tp30) REVERT: L 44 PHE cc_start: 0.7621 (m-10) cc_final: 0.7022 (m-10) REVERT: M 234 LEU cc_start: 0.6889 (mt) cc_final: 0.6650 (mt) REVERT: N 8 GLU cc_start: 0.8332 (mp0) cc_final: 0.8048 (mp0) REVERT: N 31 ASN cc_start: 0.8060 (m110) cc_final: 0.7753 (t0) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.1716 time to fit residues: 118.7277 Evaluate side-chains 448 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 0.5980 chunk 67 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN H 98 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.106023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088807 restraints weight = 58692.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091207 restraints weight = 31551.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092745 restraints weight = 20170.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093745 restraints weight = 14729.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094372 restraints weight = 11914.783| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18310 Z= 0.164 Angle : 0.766 13.382 25948 Z= 0.423 Chirality : 0.047 0.226 2924 Planarity : 0.005 0.069 2268 Dihedral : 29.246 89.730 4818 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % 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: -2.36 (0.21), residues: 1373 helix: -0.83 (0.19), residues: 694 sheet: -1.88 (1.07), residues: 26 loop : -2.39 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.034 0.002 TYR C 59 PHE 0.032 0.002 PHE K 236 TRP 0.030 0.002 TRP K 353 HIS 0.005 0.001 HIS M 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (18310) covalent geometry : angle 0.76633 / 0.42 (25948) hydrogen bonds : bond 0.05118 / 3.32 ( 821) hydrogen bonds : angle 4.48398 / 3.22 ( 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 504 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 0.568 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: A 59 GLU cc_start: 0.8273 (pm20) cc_final: 0.8062 (pm20) REVERT: A 125 LYS cc_start: 0.8631 (tppt) cc_final: 0.8187 (tppt) REVERT: A 128 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.7963 (mtp85) REVERT: B 37 LEU cc_start: 0.8858 (tp) cc_final: 0.8655 (tp) REVERT: B 67 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7348 (ttm-80) REVERT: D 42 SER cc_start: 0.8502 (m) cc_final: 0.8242 (p) REVERT: D 57 ILE cc_start: 0.8150 (mm) cc_final: 0.7849 (tp) REVERT: D 68 PHE cc_start: 0.8273 (t80) cc_final: 0.7729 (t80) REVERT: D 71 ASP cc_start: 0.7285 (p0) cc_final: 0.6604 (p0) REVERT: D 74 GLU cc_start: 0.7421 (tp30) cc_final: 0.7212 (tp30) REVERT: D 86 TYR cc_start: 0.8218 (m-10) cc_final: 0.6871 (m-10) REVERT: D 96 GLU cc_start: 0.7652 (mp0) cc_final: 0.7144 (mp0) REVERT: D 101 VAL cc_start: 0.8096 (t) cc_final: 0.7869 (p) REVERT: D 102 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7494 (ttm110) REVERT: E 60 LEU cc_start: 0.8907 (pp) cc_final: 0.8148 (pp) REVERT: E 76 GLN cc_start: 0.7367 (tp40) cc_final: 0.6888 (tp40) REVERT: F 27 GLN cc_start: 0.7744 (mp10) cc_final: 0.7303 (mp10) REVERT: F 36 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7586 (ttp-110) REVERT: F 49 LEU cc_start: 0.7791 (tt) cc_final: 0.7473 (tp) REVERT: F 58 LEU cc_start: 0.8725 (mt) cc_final: 0.8468 (mt) REVERT: F 63 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6938 (tp30) REVERT: F 78 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7764 (ptp90) REVERT: F 82 THR cc_start: 0.8468 (t) cc_final: 0.7694 (p) REVERT: F 88 TYR cc_start: 0.7129 (m-10) cc_final: 0.6741 (m-10) REVERT: G 44 ARG cc_start: 0.6516 (tpt90) cc_final: 0.6047 (tpt90) REVERT: G 67 LEU cc_start: 0.8211 (mt) cc_final: 0.7863 (mt) REVERT: G 76 LYS cc_start: 0.7301 (tptp) cc_final: 0.7091 (tptp) REVERT: G 81 THR cc_start: 0.8242 (m) cc_final: 0.7701 (p) REVERT: G 87 LEU cc_start: 0.7621 (tt) cc_final: 0.7304 (tt) REVERT: G 93 ASP cc_start: 0.7095 (t0) cc_final: 0.6665 (t0) REVERT: G 113 ASN cc_start: 0.8788 (t0) cc_final: 0.8578 (t0) REVERT: H 50 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7856 (tm-30) REVERT: H 65 LEU cc_start: 0.8161 (mm) cc_final: 0.7931 (mm) REVERT: H 74 GLU cc_start: 0.7694 (tp30) cc_final: 0.7243 (tp30) REVERT: K 170 ILE cc_start: 0.8586 (pt) cc_final: 0.8276 (mm) REVERT: K 238 GLU cc_start: 0.6669 (tt0) cc_final: 0.6226 (mm-30) REVERT: K 251 LEU cc_start: 0.8205 (mt) cc_final: 0.7619 (mp) REVERT: L 40 GLU cc_start: 0.7640 (tp30) cc_final: 0.6979 (tp30) REVERT: L 44 PHE cc_start: 0.7660 (m-10) cc_final: 0.7049 (m-10) REVERT: M 192 LEU cc_start: 0.8451 (tt) cc_final: 0.8228 (tt) REVERT: M 234 LEU cc_start: 0.6953 (mt) cc_final: 0.6724 (mt) REVERT: N 8 GLU cc_start: 0.8334 (mp0) cc_final: 0.8060 (mp0) REVERT: N 31 ASN cc_start: 0.8034 (m110) cc_final: 0.7692 (t0) outliers start: 2 outliers final: 1 residues processed: 503 average time/residue: 0.1763 time to fit residues: 123.4864 Evaluate side-chains 454 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 7.9990 chunk 96 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 0.0170 chunk 89 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.0070 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN H 98 GLN K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090497 restraints weight = 58967.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092799 restraints weight = 32216.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094286 restraints weight = 20823.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095226 restraints weight = 15284.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095872 restraints weight = 12440.183| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18310 Z= 0.156 Angle : 0.758 11.807 25948 Z= 0.419 Chirality : 0.046 0.367 2924 Planarity : 0.005 0.048 2268 Dihedral : 29.168 89.642 4818 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.08 % Allowed : 2.33 % Favored : 97.59 % 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: -2.22 (0.21), residues: 1373 helix: -0.77 (0.19), residues: 689 sheet: -1.68 (1.10), residues: 26 loop : -2.25 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 79 TYR 0.031 0.002 TYR K 214 PHE 0.034 0.002 PHE K 236 TRP 0.022 0.002 TRP K 353 HIS 0.004 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (18310) covalent geometry : angle 0.75848 / 0.42 (25948) hydrogen bonds : bond 0.04901 / 3.17 ( 821) hydrogen bonds : angle 4.43374 / 3.17 ( 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 496 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.550 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 59 GLU cc_start: 0.8130 (pm20) cc_final: 0.7891 (pm20) REVERT: A 125 LYS cc_start: 0.8673 (tppt) cc_final: 0.8180 (tppt) REVERT: A 128 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.7989 (mtp85) REVERT: B 31 LYS cc_start: 0.8029 (tppp) cc_final: 0.7742 (tppp) REVERT: C 44 ARG cc_start: 0.6204 (pmt170) cc_final: 0.5784 (pmt-80) REVERT: C 63 GLU cc_start: 0.8019 (pp20) cc_final: 0.7784 (pp20) REVERT: D 42 SER cc_start: 0.8547 (m) cc_final: 0.8305 (p) REVERT: D 46 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8290 (mmmm) REVERT: D 68 PHE cc_start: 0.8206 (t80) cc_final: 0.7644 (t80) REVERT: D 71 ASP cc_start: 0.7369 (p0) cc_final: 0.6720 (p0) REVERT: D 74 GLU cc_start: 0.7591 (tp30) cc_final: 0.7230 (tp30) REVERT: D 96 GLU cc_start: 0.7590 (mp0) cc_final: 0.7131 (mp0) REVERT: D 101 VAL cc_start: 0.8053 (t) cc_final: 0.7808 (p) REVERT: D 102 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7375 (ttm110) REVERT: D 124 TYR cc_start: 0.7402 (t80) cc_final: 0.7122 (t80) REVERT: E 45 THR cc_start: 0.7450 (p) cc_final: 0.6830 (p) REVERT: E 48 LEU cc_start: 0.7943 (mt) cc_final: 0.7641 (mp) REVERT: E 60 LEU cc_start: 0.8894 (pp) cc_final: 0.8111 (pp) REVERT: E 68 GLN cc_start: 0.7556 (tt0) cc_final: 0.7324 (tp-100) REVERT: E 76 GLN cc_start: 0.7411 (tp40) cc_final: 0.6878 (tp40) REVERT: E 125 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7308 (mtmm) REVERT: F 44 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8145 (mmtt) REVERT: F 58 LEU cc_start: 0.8742 (mt) cc_final: 0.8515 (mt) REVERT: F 63 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6965 (tp30) REVERT: F 78 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7783 (ptp90) REVERT: F 82 THR cc_start: 0.8512 (t) cc_final: 0.7700 (p) REVERT: F 88 TYR cc_start: 0.7072 (m-10) cc_final: 0.6731 (m-10) REVERT: G 30 ARG cc_start: 0.7023 (ttp-110) cc_final: 0.6817 (mtm-85) REVERT: G 67 LEU cc_start: 0.8126 (mt) cc_final: 0.7671 (mt) REVERT: G 76 LYS cc_start: 0.7362 (tptp) cc_final: 0.7110 (tptp) REVERT: G 81 THR cc_start: 0.8178 (m) cc_final: 0.7647 (p) REVERT: G 87 LEU cc_start: 0.7792 (tt) cc_final: 0.7390 (tt) REVERT: G 93 ASP cc_start: 0.6925 (t0) cc_final: 0.6019 (t0) REVERT: H 37 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7536 (ttpp) REVERT: H 50 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 74 GLU cc_start: 0.7712 (tp30) cc_final: 0.7199 (tp30) REVERT: H 118 THR cc_start: 0.8650 (t) cc_final: 0.8381 (p) REVERT: K 199 ASP cc_start: 0.7385 (p0) cc_final: 0.6714 (p0) REVERT: K 238 GLU cc_start: 0.6647 (tt0) cc_final: 0.6229 (mm-30) REVERT: K 251 LEU cc_start: 0.8165 (mt) cc_final: 0.7843 (mm) REVERT: K 292 LYS cc_start: 0.7126 (mmmt) cc_final: 0.6921 (mmmm) REVERT: K 357 LEU cc_start: 0.8076 (mt) cc_final: 0.7763 (mt) REVERT: K 364 HIS cc_start: 0.7064 (t70) cc_final: 0.6716 (t-170) REVERT: K 372 GLU cc_start: 0.7961 (tt0) cc_final: 0.7739 (tt0) REVERT: L 40 GLU cc_start: 0.7500 (tp30) cc_final: 0.7270 (tp30) REVERT: N 31 ASN cc_start: 0.7954 (m110) cc_final: 0.7631 (t0) outliers start: 1 outliers final: 0 residues processed: 495 average time/residue: 0.1782 time to fit residues: 122.1565 Evaluate side-chains 455 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 0.5980 chunk 70 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 356 ASN N 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.103792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086908 restraints weight = 59344.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089088 restraints weight = 33815.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.090485 restraints weight = 22571.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091424 restraints weight = 17044.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092026 restraints weight = 14069.374| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 18310 Z= 0.266 Angle : 0.903 12.148 25948 Z= 0.494 Chirality : 0.052 0.245 2924 Planarity : 0.007 0.081 2268 Dihedral : 29.127 89.236 4818 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -2.36 (0.21), residues: 1373 helix: -0.81 (0.19), residues: 701 sheet: -1.94 (1.13), residues: 26 loop : -2.42 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 21 TYR 0.033 0.003 TYR K 214 PHE 0.055 0.003 PHE K 236 TRP 0.023 0.002 TRP K 353 HIS 0.010 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.27 (18310) covalent geometry : angle 0.90337 / 0.49 (25948) hydrogen bonds : bond 0.06814 / 4.40 ( 821) hydrogen bonds : angle 4.52036 / 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 527 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.516 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 74 ILE cc_start: 0.8670 (tp) cc_final: 0.8296 (tp) REVERT: A 97 GLU cc_start: 0.7527 (tp30) cc_final: 0.6829 (tp30) REVERT: A 125 LYS cc_start: 0.8608 (tppt) cc_final: 0.8240 (tppt) REVERT: B 37 LEU cc_start: 0.8845 (tp) cc_final: 0.8466 (tp) REVERT: B 59 LYS cc_start: 0.8982 (tppp) cc_final: 0.8745 (tppp) REVERT: B 67 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: B 88 TYR cc_start: 0.8563 (m-10) cc_final: 0.8347 (m-80) REVERT: C 59 TYR cc_start: 0.7149 (m-80) cc_final: 0.6673 (m-10) REVERT: C 63 GLU cc_start: 0.7867 (pp20) cc_final: 0.7584 (pp20) REVERT: D 42 SER cc_start: 0.8471 (m) cc_final: 0.8260 (p) REVERT: D 71 ASP cc_start: 0.7198 (p0) cc_final: 0.6505 (p0) REVERT: D 74 GLU cc_start: 0.7364 (tp30) cc_final: 0.6828 (tp30) REVERT: D 96 GLU cc_start: 0.7457 (mp0) cc_final: 0.7076 (mp0) REVERT: D 101 VAL cc_start: 0.8489 (t) cc_final: 0.8247 (p) REVERT: D 102 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7737 (ttm110) REVERT: E 45 THR cc_start: 0.8050 (p) cc_final: 0.7843 (p) REVERT: E 76 GLN cc_start: 0.7425 (tp40) cc_final: 0.6954 (tp40) REVERT: F 44 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8203 (mmtt) REVERT: F 58 LEU cc_start: 0.8662 (mt) cc_final: 0.8424 (mm) REVERT: F 63 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6748 (tp30) REVERT: F 88 TYR cc_start: 0.7414 (m-10) cc_final: 0.6828 (m-10) REVERT: F 95 ARG cc_start: 0.7659 (ptp-170) cc_final: 0.7319 (ptt-90) REVERT: G 67 LEU cc_start: 0.8238 (mt) cc_final: 0.7806 (mt) REVERT: G 79 ARG cc_start: 0.6925 (tpm170) cc_final: 0.6667 (mmp-170) REVERT: G 80 ILE cc_start: 0.8115 (tt) cc_final: 0.7886 (tt) REVERT: G 81 THR cc_start: 0.8554 (m) cc_final: 0.8122 (p) REVERT: G 87 LEU cc_start: 0.7790 (tt) cc_final: 0.6389 (tt) REVERT: H 62 MET cc_start: 0.7327 (mmm) cc_final: 0.7091 (tpp) REVERT: H 64 ILE cc_start: 0.8519 (mm) cc_final: 0.8307 (mm) REVERT: H 65 LEU cc_start: 0.8144 (mm) cc_final: 0.7873 (mm) REVERT: K 251 LEU cc_start: 0.8336 (mt) cc_final: 0.8000 (mm) REVERT: K 274 TYR cc_start: 0.7844 (m-10) cc_final: 0.7614 (m-10) REVERT: K 290 PHE cc_start: 0.6586 (p90) cc_final: 0.5867 (p90) REVERT: K 357 LEU cc_start: 0.8328 (mt) cc_final: 0.8114 (mt) REVERT: L 40 GLU cc_start: 0.7650 (tp30) cc_final: 0.7250 (tp30) REVERT: M 234 LEU cc_start: 0.6925 (mt) cc_final: 0.6688 (mt) REVERT: M 278 TYR cc_start: 0.5765 (t80) cc_final: 0.5494 (t80) REVERT: N 8 GLU cc_start: 0.8250 (mp0) cc_final: 0.7958 (mp0) REVERT: N 31 ASN cc_start: 0.7934 (m110) cc_final: 0.7549 (t0) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.1781 time to fit residues: 129.6001 Evaluate side-chains 465 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 0.2980 chunk 22 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 0.0670 chunk 157 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 108 ASN H 98 GLN K 285 HIS ** K 312 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089345 restraints weight = 59206.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091520 restraints weight = 33532.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.092950 restraints weight = 22343.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093882 restraints weight = 16844.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094485 restraints weight = 13948.482| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18310 Z= 0.171 Angle : 0.805 12.225 25948 Z= 0.442 Chirality : 0.048 0.283 2924 Planarity : 0.006 0.084 2268 Dihedral : 29.097 88.818 4818 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.08 % Allowed : 1.52 % Favored : 98.39 % 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: -2.23 (0.21), residues: 1373 helix: -0.69 (0.19), residues: 704 sheet: -2.32 (1.07), residues: 26 loop : -2.36 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 49 TYR 0.030 0.002 TYR K 214 PHE 0.040 0.002 PHE K 290 TRP 0.026 0.002 TRP K 353 HIS 0.007 0.001 HIS K 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (18310) covalent geometry : angle 0.80477 / 0.44 (25948) hydrogen bonds : bond 0.05122 / 3.29 ( 821) hydrogen bonds : angle 4.47644 / 3.21 ( 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 510 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 509 time to evaluate : 0.493 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: A 70 LEU cc_start: 0.8578 (tt) cc_final: 0.8366 (tp) REVERT: A 73 GLU cc_start: 0.7338 (pt0) cc_final: 0.6973 (pt0) REVERT: A 97 GLU cc_start: 0.7456 (tp30) cc_final: 0.6973 (tp30) REVERT: A 125 LYS cc_start: 0.8578 (tppt) cc_final: 0.8150 (tppt) REVERT: B 53 GLU cc_start: 0.7731 (pp20) cc_final: 0.7392 (pp20) REVERT: C 63 GLU cc_start: 0.7919 (pp20) cc_final: 0.7688 (pp20) REVERT: D 86 TYR cc_start: 0.8352 (m-10) cc_final: 0.7612 (m-10) REVERT: D 95 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8057 (ttt-90) REVERT: E 45 THR cc_start: 0.8091 (p) cc_final: 0.7843 (p) REVERT: E 65 LEU cc_start: 0.8394 (tp) cc_final: 0.8123 (mm) REVERT: E 76 GLN cc_start: 0.7315 (tp40) cc_final: 0.6767 (tp-100) REVERT: E 96 VAL cc_start: 0.8401 (p) cc_final: 0.8039 (p) REVERT: E 129 ARG cc_start: 0.8099 (tpt90) cc_final: 0.7813 (tpt90) REVERT: F 58 LEU cc_start: 0.8675 (mt) cc_final: 0.8455 (mt) REVERT: F 63 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6874 (mm-30) REVERT: F 78 ARG cc_start: 0.8565 (mtm110) cc_final: 0.7776 (ptp90) REVERT: F 88 TYR cc_start: 0.7383 (m-10) cc_final: 0.6813 (m-10) REVERT: G 44 ARG cc_start: 0.7075 (tpt170) cc_final: 0.6826 (tpt-90) REVERT: G 67 LEU cc_start: 0.8139 (mt) cc_final: 0.7733 (mt) REVERT: G 81 THR cc_start: 0.8509 (m) cc_final: 0.8277 (p) REVERT: G 87 LEU cc_start: 0.7581 (tt) cc_final: 0.7168 (tt) REVERT: G 113 ASN cc_start: 0.8789 (t0) cc_final: 0.8537 (t0) REVERT: K 269 ASP cc_start: 0.8139 (m-30) cc_final: 0.7932 (m-30) REVERT: K 357 LEU cc_start: 0.8322 (mt) cc_final: 0.8088 (mt) REVERT: K 364 HIS cc_start: 0.7184 (t70) cc_final: 0.6956 (t70) REVERT: L 40 GLU cc_start: 0.7632 (tp30) cc_final: 0.7289 (tp30) REVERT: M 209 MET cc_start: 0.6113 (ttp) cc_final: 0.5878 (ttp) REVERT: M 234 LEU cc_start: 0.6892 (mt) cc_final: 0.6680 (mt) REVERT: M 264 LEU cc_start: 0.7961 (tt) cc_final: 0.7699 (mt) REVERT: M 280 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7977 (mmt180) REVERT: N 7 LEU cc_start: 0.8403 (pp) cc_final: 0.8048 (pp) REVERT: N 8 GLU cc_start: 0.8243 (mp0) cc_final: 0.7755 (mp0) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.1749 time to fit residues: 122.4193 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 : 0.318 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 38 HIS D 50 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 91 ASN N 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.105736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088894 restraints weight = 59477.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091066 restraints weight = 33867.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092452 restraints weight = 22611.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093356 restraints weight = 17071.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093883 restraints weight = 14202.822| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 18310 Z= 0.191 Angle : 0.833 12.433 25948 Z= 0.458 Chirality : 0.049 0.225 2924 Planarity : 0.006 0.076 2268 Dihedral : 29.076 88.116 4818 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.08 % Allowed : 0.48 % Favored : 99.44 % 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: -2.30 (0.21), residues: 1373 helix: -0.82 (0.19), residues: 697 sheet: -2.01 (1.09), residues: 26 loop : -2.32 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 78 TYR 0.032 0.003 TYR C 59 PHE 0.041 0.002 PHE K 237 TRP 0.033 0.002 TRP K 353 HIS 0.012 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (18310) covalent geometry : angle 0.83348 / 0.46 (25948) hydrogen bonds : bond 0.05411 / 3.50 ( 821) hydrogen bonds : angle 4.57968 / 3.29 ( 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 507 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 506 time to evaluate : 0.482 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: A 73 GLU cc_start: 0.7378 (pt0) cc_final: 0.7125 (pt0) REVERT: A 97 GLU cc_start: 0.7419 (tp30) cc_final: 0.7138 (tp30) REVERT: A 125 LYS cc_start: 0.8506 (tppt) cc_final: 0.8155 (tppt) REVERT: B 36 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7758 (mtm-85) REVERT: B 53 GLU cc_start: 0.7747 (pp20) cc_final: 0.7437 (pp20) REVERT: C 31 ILE cc_start: 0.8497 (mm) cc_final: 0.7923 (mm) REVERT: C 63 GLU cc_start: 0.7934 (pp20) cc_final: 0.7714 (pp20) REVERT: D 46 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8112 (mmpt) REVERT: D 86 TYR cc_start: 0.8378 (m-10) cc_final: 0.7190 (m-10) REVERT: D 95 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.7917 (ttt-90) REVERT: E 59 GLU cc_start: 0.7862 (tp30) cc_final: 0.7618 (tp30) REVERT: E 76 GLN cc_start: 0.7409 (tp40) cc_final: 0.6886 (tp-100) REVERT: E 125 LYS cc_start: 0.7772 (ptpp) cc_final: 0.7451 (pttp) REVERT: E 129 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7940 (tpt90) REVERT: F 63 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6843 (mm-30) REVERT: F 78 ARG cc_start: 0.8455 (mtm110) cc_final: 0.7851 (ptp90) REVERT: F 88 TYR cc_start: 0.7362 (m-10) cc_final: 0.6907 (m-10) REVERT: F 95 ARG cc_start: 0.7398 (ptp-170) cc_final: 0.7164 (ptp90) REVERT: G 67 LEU cc_start: 0.8168 (mt) cc_final: 0.7646 (mt) REVERT: G 81 THR cc_start: 0.8455 (m) cc_final: 0.8201 (p) REVERT: G 87 LEU cc_start: 0.7633 (tt) cc_final: 0.7165 (tt) REVERT: G 113 ASN cc_start: 0.8764 (t0) cc_final: 0.8551 (t0) REVERT: H 123 LYS cc_start: 0.8861 (pttt) cc_final: 0.8366 (pptt) REVERT: K 199 ASP cc_start: 0.7820 (p0) cc_final: 0.6732 (p0) REVERT: K 357 LEU cc_start: 0.8318 (mt) cc_final: 0.8100 (mt) REVERT: K 364 HIS cc_start: 0.7228 (t70) cc_final: 0.6999 (t70) REVERT: L 40 GLU cc_start: 0.7626 (tp30) cc_final: 0.7321 (tp30) REVERT: M 209 MET cc_start: 0.6109 (ttp) cc_final: 0.5800 (ttp) REVERT: M 264 LEU cc_start: 0.8071 (tt) cc_final: 0.7842 (mt) REVERT: N 7 LEU cc_start: 0.8442 (pp) cc_final: 0.8067 (pp) REVERT: N 8 GLU cc_start: 0.8260 (mp0) cc_final: 0.7772 (mp0) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.1798 time to fit residues: 125.1698 Evaluate side-chains 467 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 0.0870 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089925 restraints weight = 60020.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091915 restraints weight = 35173.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093230 restraints weight = 24065.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094064 restraints weight = 18537.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094614 restraints weight = 15612.493| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18310 Z= 0.176 Angle : 0.823 17.180 25948 Z= 0.451 Chirality : 0.048 0.225 2924 Planarity : 0.006 0.076 2268 Dihedral : 29.056 88.023 4818 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -2.16 (0.22), residues: 1373 helix: -0.66 (0.19), residues: 686 sheet: -1.89 (1.08), residues: 26 loop : -2.27 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG F 67 TYR 0.029 0.002 TYR K 352 PHE 0.035 0.002 PHE K 237 TRP 0.029 0.002 TRP K 353 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (18310) covalent geometry : angle 0.82324 / 0.45 (25948) hydrogen bonds : bond 0.05180 / 3.33 ( 821) hydrogen bonds : angle 4.52895 / 3.25 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.97 seconds wall clock time: 63 minutes 13.06 seconds (3793.06 seconds total)