Starting phenix.real_space_refine on Sun Aug 24 17:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2y_38022/08_2025/8x2y_38022.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5443 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 22 5.16 5 C 10104 2.51 5 N 3123 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.45, per 1000 atoms: 0.26 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: 1.48 Conformation dependent library (CDL) restraints added in 882.9 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 3.00 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: 4.15 Time building geometry restraints manager: 2.06 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=" 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=" C ASP K 269 " pdb=" N PRO K 270 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.373 0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" CG ARG F 92 " pdb=" CD ARG F 92 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 ... (remaining 18305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 24330 1.92 - 3.84: 1407 3.84 - 5.76: 144 5.76 - 7.69: 52 7.69 - 9.61: 15 Bond angle restraints: 25948 Sorted by residual: angle pdb=" C ILE F 46 " pdb=" N SER F 47 " pdb=" CA SER F 47 " ideal model delta sigma weight residual 121.54 131.15 -9.61 1.91e+00 2.74e-01 2.53e+01 angle pdb=" CA THR C 61 " pdb=" C THR C 61 " pdb=" O THR C 61 " ideal model delta sigma weight residual 120.70 115.72 4.98 1.03e+00 9.43e-01 2.34e+01 angle pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " ideal model delta sigma weight residual 114.10 122.83 -8.73 2.00e+00 2.50e-01 1.91e+01 angle pdb=" C PHE M 136 " pdb=" CA PHE M 136 " pdb=" CB PHE M 136 " ideal model delta sigma weight residual 110.42 102.18 8.24 1.99e+00 2.53e-01 1.71e+01 angle pdb=" N GLY H 107 " pdb=" CA GLY H 107 " pdb=" C GLY H 107 " ideal model delta sigma weight residual 113.18 122.72 -9.54 2.37e+00 1.78e-01 1.62e+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: 1988 0.050 - 0.100: 727 0.100 - 0.149: 170 0.149 - 0.199: 32 0.199 - 0.249: 7 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=" 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 chirality pdb=" CG LEU E 92 " pdb=" CB LEU E 92 " pdb=" CD1 LEU E 92 " pdb=" CD2 LEU E 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.000 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18310 Z= 0.300 Angle : 0.991 9.607 25948 Z= 0.560 Chirality : 0.055 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 aren 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 covalent geometry : bond 0.00623 (18310) covalent geometry : angle 0.99098 (25948) hydrogen bonds : bond 0.17855 ( 821) hydrogen bonds : angle 7.17455 ( 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 : 0.531 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: 0.7635 (tp) cc_final: 0.7253 (tp) REVERT: E 46 VAL cc_start: 0.7292 (p) cc_final: 0.7029 (m) REVERT: E 62 ILE cc_start: 0.6464 (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: 0.7622 (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: 0.8453 (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: 0.6403 (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: 0.1522 time to fit residues: 117.0103 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 : 0.388 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 66 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN K 312 GLN L 20 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 ASN M 201 HIS M 260 ASN N 102 ASN N 107 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089849 restraints weight = 58334.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092340 restraints weight = 30848.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093952 restraints weight = 19404.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095003 restraints weight = 13881.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095693 restraints weight = 11029.818| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18310 Z= 0.183 Angle : 0.756 11.625 25948 Z= 0.421 Chirality : 0.042 0.164 2924 Planarity : 0.005 0.052 2268 Dihedral : 29.320 89.864 4818 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.48 % Allowed : 5.86 % Favored : 93.66 % 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 aren not related in a simple way. whole: -3.20 (0.20), residues: 1373 helix: -1.71 (0.17), residues: 695 sheet: -2.39 (0.95), residues: 26 loop : -2.56 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 128 TYR 0.029 0.002 TYR F 98 PHE 0.023 0.002 PHE E 54 TRP 0.015 0.002 TRP K 247 HIS 0.011 0.001 HIS M 338 Details of bonding type rmsd covalent geometry : bond 0.00397 (18310) covalent geometry : angle 0.75620 (25948) hydrogen bonds : bond 0.05055 ( 821) hydrogen bonds : angle 4.77737 ( 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 507 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 501 time to evaluate : 0.457 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 54 PHE cc_start: 0.8506 (m-10) cc_final: 0.8305 (m-80) REVERT: A 125 LYS cc_start: 0.8491 (tppt) cc_final: 0.7955 (tppt) REVERT: B 37 LEU cc_start: 0.8838 (tp) cc_final: 0.8430 (tp) REVERT: B 78 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.7019 (ttp-110) REVERT: C 74 ASP cc_start: 0.7770 (t0) cc_final: 0.7391 (t0) REVERT: D 42 SER cc_start: 0.8591 (m) cc_final: 0.8160 (p) REVERT: D 51 THR cc_start: 0.7903 (p) cc_final: 0.7702 (p) REVERT: D 57 ILE cc_start: 0.7254 (mm) cc_final: 0.6873 (tp) REVERT: D 88 LYS cc_start: 0.8274 (mmmm) cc_final: 0.8050 (mmmm) REVERT: D 98 GLN cc_start: 0.7823 (tp40) cc_final: 0.7380 (tp40) REVERT: E 83 ARG cc_start: 0.7313 (tpm170) cc_final: 0.7031 (mmm160) REVERT: E 120 GLN cc_start: 0.5684 (mp-120) cc_final: 0.5466 (mp10) REVERT: F 27 GLN cc_start: 0.7716 (mp-120) cc_final: 0.5758 (mp10) REVERT: F 49 LEU cc_start: 0.6942 (tt) cc_final: 0.6488 (tp) REVERT: F 63 GLU cc_start: 0.7111 (tp30) cc_final: 0.6339 (tp30) REVERT: F 82 THR cc_start: 0.8043 (t) cc_final: 0.7011 (p) REVERT: G 67 LEU cc_start: 0.7645 (mt) cc_final: 0.7099 (mt) REVERT: G 70 ASN cc_start: 0.6424 (p0) cc_final: 0.5787 (p0) REVERT: G 80 ILE cc_start: 0.7458 (tt) cc_final: 0.7231 (tt) REVERT: H 43 TYR cc_start: 0.5210 (m-80) cc_final: 0.4859 (m-10) REVERT: H 63 SER cc_start: 0.8123 (t) cc_final: 0.7639 (p) REVERT: H 74 GLU cc_start: 0.7479 (tp30) cc_final: 0.7233 (tp30) REVERT: K 167 LEU cc_start: 0.8615 (mm) cc_final: 0.8111 (tp) REVERT: K 251 LEU cc_start: 0.7967 (mt) cc_final: 0.7600 (mt) REVERT: K 269 ASP cc_start: 0.8593 (m-30) cc_final: 0.8314 (m-30) REVERT: K 274 TYR cc_start: 0.7205 (m-10) cc_final: 0.6987 (m-10) REVERT: K 364 HIS cc_start: 0.6690 (t-90) cc_final: 0.6382 (t-90) REVERT: L 40 GLU cc_start: 0.6943 (tm-30) cc_final: 0.5624 (tm-30) REVERT: L 44 PHE cc_start: 0.7413 (m-10) cc_final: 0.6977 (m-10) REVERT: M 141 PHE cc_start: 0.7924 (p90) cc_final: 0.7681 (p90) REVERT: M 234 LEU cc_start: 0.6783 (mt) cc_final: 0.6573 (mt) REVERT: N 8 GLU cc_start: 0.8313 (mp0) cc_final: 0.7910 (mp0) REVERT: N 31 ASN cc_start: 0.8325 (m110) cc_final: 0.7822 (t0) REVERT: N 96 LEU cc_start: 0.8458 (pp) cc_final: 0.8090 (pp) outliers start: 6 outliers final: 0 residues processed: 503 average time/residue: 0.1531 time to fit residues: 107.2647 Evaluate side-chains 435 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 1.9990 chunk 120 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN F 27 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.104236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087069 restraints weight = 58595.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089511 restraints weight = 31172.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091104 restraints weight = 19763.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.092133 restraints weight = 14290.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092760 restraints weight = 11442.518| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18310 Z= 0.247 Angle : 0.836 10.769 25948 Z= 0.462 Chirality : 0.046 0.236 2924 Planarity : 0.007 0.101 2268 Dihedral : 28.997 89.776 4818 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.48 % Allowed : 7.78 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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 aren not related in a simple way. whole: -2.82 (0.20), residues: 1373 helix: -1.27 (0.17), residues: 707 sheet: -1.91 (1.12), residues: 26 loop : -2.57 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 279 TYR 0.050 0.003 TYR F 98 PHE 0.025 0.003 PHE K 236 TRP 0.015 0.002 TRP K 353 HIS 0.006 0.001 HIS G 111 Details of bonding type rmsd covalent geometry : bond 0.00540 (18310) covalent geometry : angle 0.83571 (25948) hydrogen bonds : bond 0.06265 ( 821) hydrogen bonds : angle 4.59104 ( 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 540 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 534 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8691 (m-10) cc_final: 0.8394 (m-80) REVERT: A 60 LEU cc_start: 0.8902 (mm) cc_final: 0.8683 (mt) REVERT: A 69 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.7897 (ttm110) REVERT: A 74 ILE cc_start: 0.8663 (tp) cc_final: 0.8306 (tp) REVERT: A 97 GLU cc_start: 0.7537 (tp30) cc_final: 0.7317 (tp30) REVERT: A 125 LYS cc_start: 0.8668 (tppt) cc_final: 0.8231 (tppt) REVERT: B 36 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7701 (mtm110) REVERT: B 55 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8444 (mtt180) REVERT: C 63 GLU cc_start: 0.8040 (pp20) cc_final: 0.7209 (tm-30) REVERT: C 84 HIS cc_start: 0.7425 (t-90) cc_final: 0.6857 (t-170) REVERT: C 92 ASP cc_start: 0.8500 (t0) cc_final: 0.8299 (t0) REVERT: C 113 ASN cc_start: 0.7808 (p0) cc_final: 0.7599 (p0) REVERT: D 71 ASP cc_start: 0.7471 (m-30) cc_final: 0.7224 (m-30) REVERT: D 96 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 98 GLN cc_start: 0.8088 (tp40) cc_final: 0.7878 (tp40) REVERT: D 102 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7917 (ttm170) REVERT: E 45 THR cc_start: 0.8012 (p) cc_final: 0.7647 (p) REVERT: E 59 GLU cc_start: 0.8283 (tp30) cc_final: 0.8011 (tp30) REVERT: E 70 LEU cc_start: 0.8606 (mm) cc_final: 0.8337 (tp) REVERT: E 76 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7184 (tp40) REVERT: E 78 PHE cc_start: 0.8366 (m-10) cc_final: 0.8012 (m-10) REVERT: E 123 ASP cc_start: 0.8003 (m-30) cc_final: 0.7748 (m-30) REVERT: F 50 ILE cc_start: 0.8536 (pt) cc_final: 0.8295 (mt) REVERT: F 61 PHE cc_start: 0.8725 (t80) cc_final: 0.8524 (t80) REVERT: F 63 GLU cc_start: 0.7360 (tp30) cc_final: 0.7034 (tp30) REVERT: F 78 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8348 (ptp90) REVERT: F 88 TYR cc_start: 0.7441 (m-10) cc_final: 0.6953 (m-10) REVERT: G 44 ARG cc_start: 0.7402 (tpt90) cc_final: 0.7041 (tpt170) REVERT: G 67 LEU cc_start: 0.8142 (mt) cc_final: 0.7906 (mt) REVERT: G 70 ASN cc_start: 0.7677 (p0) cc_final: 0.7364 (p0) REVERT: G 81 THR cc_start: 0.8551 (m) cc_final: 0.8068 (p) REVERT: G 94 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7701 (mm-30) REVERT: G 113 ASN cc_start: 0.8879 (t0) cc_final: 0.8393 (t0) REVERT: H 46 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7845 (ttpt) REVERT: H 65 LEU cc_start: 0.8375 (mm) cc_final: 0.7966 (mm) REVERT: H 74 GLU cc_start: 0.7655 (tp30) cc_final: 0.7408 (tp30) REVERT: H 89 LYS cc_start: 0.8630 (tppp) cc_final: 0.8267 (mmmt) REVERT: H 118 THR cc_start: 0.8624 (t) cc_final: 0.8395 (p) REVERT: K 170 ILE cc_start: 0.8392 (mt) cc_final: 0.7776 (mm) REVERT: K 269 ASP cc_start: 0.8460 (m-30) cc_final: 0.8220 (m-30) REVERT: K 311 TYR cc_start: 0.6547 (m-10) cc_final: 0.6168 (m-10) REVERT: K 356 THR cc_start: 0.8371 (m) cc_final: 0.8047 (m) REVERT: K 364 HIS cc_start: 0.7005 (t-90) cc_final: 0.6685 (t-90) REVERT: K 381 THR cc_start: 0.9037 (m) cc_final: 0.8555 (t) REVERT: K 406 ASN cc_start: 0.7309 (p0) cc_final: 0.7094 (p0) REVERT: L 40 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6578 (tm-30) REVERT: L 44 PHE cc_start: 0.7753 (m-10) cc_final: 0.7314 (m-10) REVERT: M 141 PHE cc_start: 0.8340 (p90) cc_final: 0.8118 (p90) REVERT: M 209 MET cc_start: 0.6370 (ttp) cc_final: 0.5985 (ttp) REVERT: M 217 PHE cc_start: 0.7139 (t80) cc_final: 0.6902 (t80) REVERT: M 353 LYS cc_start: 0.9019 (mptt) cc_final: 0.8812 (mptt) REVERT: N 8 GLU cc_start: 0.8309 (mp0) cc_final: 0.7912 (mp0) outliers start: 6 outliers final: 1 residues processed: 535 average time/residue: 0.1610 time to fit residues: 118.6869 Evaluate side-chains 465 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 3.9990 chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 75 HIS H 59 GLN H 98 GLN K 284 HIS K 312 GLN K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.102152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.085480 restraints weight = 58896.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087513 restraints weight = 34323.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088854 restraints weight = 23298.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089731 restraints weight = 17771.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090281 restraints weight = 14837.921| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 18310 Z= 0.317 Angle : 0.859 11.297 25948 Z= 0.477 Chirality : 0.048 0.204 2924 Planarity : 0.007 0.090 2268 Dihedral : 29.045 89.643 4818 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.24 % Allowed : 5.86 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.21), residues: 1373 helix: -0.97 (0.18), residues: 716 sheet: -2.42 (1.15), residues: 26 loop : -2.52 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 63 TYR 0.040 0.003 TYR F 98 PHE 0.045 0.003 PHE K 236 TRP 0.040 0.004 TRP K 353 HIS 0.012 0.002 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00711 (18310) covalent geometry : angle 0.85884 (25948) hydrogen bonds : bond 0.06408 ( 821) hydrogen bonds : angle 4.50923 ( 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 536 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 533 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7531 (mtp180) REVERT: A 58 THR cc_start: 0.8840 (p) cc_final: 0.8613 (p) REVERT: A 59 GLU cc_start: 0.8304 (pm20) cc_final: 0.8063 (pm20) REVERT: A 62 ILE cc_start: 0.8941 (mm) cc_final: 0.8622 (mt) REVERT: A 69 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8226 (ttp-110) REVERT: B 25 ASN cc_start: 0.8157 (m-40) cc_final: 0.7708 (m-40) REVERT: B 31 LYS cc_start: 0.8723 (tppp) cc_final: 0.8311 (tppp) REVERT: B 69 SER cc_start: 0.8695 (m) cc_final: 0.8393 (p) REVERT: C 63 GLU cc_start: 0.7869 (pp20) cc_final: 0.6845 (tm-30) REVERT: C 84 HIS cc_start: 0.7527 (t-90) cc_final: 0.6935 (t-170) REVERT: D 71 ASP cc_start: 0.7308 (m-30) cc_final: 0.7020 (m-30) REVERT: D 86 TYR cc_start: 0.8253 (m-10) cc_final: 0.7635 (m-10) REVERT: D 109 LEU cc_start: 0.8988 (tp) cc_final: 0.8450 (tp) REVERT: E 48 LEU cc_start: 0.8370 (mp) cc_final: 0.7693 (mp) REVERT: E 63 ARG cc_start: 0.7912 (tpt90) cc_final: 0.7590 (mmm160) REVERT: E 64 LYS cc_start: 0.8479 (mtpp) cc_final: 0.7673 (mtpt) REVERT: E 65 LEU cc_start: 0.8451 (tt) cc_final: 0.8085 (mm) REVERT: E 70 LEU cc_start: 0.8542 (mm) cc_final: 0.8301 (tp) REVERT: E 73 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6156 (mt-10) REVERT: E 76 GLN cc_start: 0.7488 (tp-100) cc_final: 0.7187 (tp40) REVERT: F 61 PHE cc_start: 0.8561 (t80) cc_final: 0.8288 (t80) REVERT: F 78 ARG cc_start: 0.8707 (mtm110) cc_final: 0.8459 (mtm110) REVERT: F 88 TYR cc_start: 0.7689 (m-10) cc_final: 0.7125 (m-10) REVERT: G 66 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6919 (tm-30) REVERT: G 67 LEU cc_start: 0.8172 (mt) cc_final: 0.7914 (mt) REVERT: G 81 THR cc_start: 0.8584 (m) cc_final: 0.8320 (p) REVERT: G 87 LEU cc_start: 0.6804 (tp) cc_final: 0.6048 (tp) REVERT: G 94 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7803 (mm-30) REVERT: H 44 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7964 (tp) REVERT: H 89 LYS cc_start: 0.8860 (tppp) cc_final: 0.8636 (mmmt) REVERT: H 111 LYS cc_start: 0.8473 (pttm) cc_final: 0.8179 (ptpp) REVERT: K 170 ILE cc_start: 0.8211 (mt) cc_final: 0.7976 (pt) REVERT: K 172 MET cc_start: 0.6664 (pmm) cc_final: 0.6359 (pmm) REVERT: K 221 ARG cc_start: 0.5652 (ttt180) cc_final: 0.4898 (ttt180) REVERT: K 250 ASN cc_start: 0.7929 (p0) cc_final: 0.7677 (p0) REVERT: K 251 LEU cc_start: 0.8446 (mm) cc_final: 0.8131 (mm) REVERT: K 269 ASP cc_start: 0.8293 (m-30) cc_final: 0.8052 (m-30) REVERT: K 305 ILE cc_start: 0.8904 (tt) cc_final: 0.8488 (pt) REVERT: K 310 GLN cc_start: 0.7133 (pp30) cc_final: 0.6764 (pp30) REVERT: M 141 PHE cc_start: 0.8163 (p90) cc_final: 0.7930 (p90) REVERT: M 209 MET cc_start: 0.6565 (ttp) cc_final: 0.6204 (ttp) REVERT: M 218 GLU cc_start: 0.7821 (tp30) cc_final: 0.7615 (tp30) REVERT: M 353 LYS cc_start: 0.9118 (mptt) cc_final: 0.8813 (mptt) REVERT: N 8 GLU cc_start: 0.8368 (mp0) cc_final: 0.8071 (mp0) outliers start: 3 outliers final: 1 residues processed: 534 average time/residue: 0.1729 time to fit residues: 125.2140 Evaluate side-chains 480 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 478 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 3.9990 chunk 99 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN F 27 GLN G 38 HIS H 98 GLN K 203 GLN K 312 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS M 204 GLN N 91 ASN N 102 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.105183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088404 restraints weight = 59175.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090427 restraints weight = 34705.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091761 restraints weight = 23718.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092633 restraints weight = 18275.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093168 restraints weight = 15338.817| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.7561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18310 Z= 0.184 Angle : 0.738 11.072 25948 Z= 0.408 Chirality : 0.042 0.216 2924 Planarity : 0.005 0.073 2268 Dihedral : 28.926 88.391 4818 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.32 % Allowed : 4.09 % Favored : 95.59 % 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 aren not related in a simple way. whole: -2.31 (0.22), residues: 1373 helix: -0.80 (0.19), residues: 721 sheet: -2.53 (1.10), residues: 26 loop : -2.36 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 40 TYR 0.022 0.002 TYR H 43 PHE 0.030 0.002 PHE N 21 TRP 0.028 0.003 TRP K 353 HIS 0.006 0.001 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00409 (18310) covalent geometry : angle 0.73804 (25948) hydrogen bonds : bond 0.04910 ( 821) hydrogen bonds : angle 4.28669 ( 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 538 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 534 time to evaluate : 0.519 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 62 ILE cc_start: 0.8742 (mm) cc_final: 0.8494 (mt) REVERT: A 69 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8084 (ttp-110) REVERT: A 106 ASP cc_start: 0.7269 (m-30) cc_final: 0.6465 (m-30) REVERT: B 52 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 53 GLU cc_start: 0.7434 (pp20) cc_final: 0.6758 (pp20) REVERT: C 63 GLU cc_start: 0.7737 (pp20) cc_final: 0.6839 (tm-30) REVERT: C 84 HIS cc_start: 0.7456 (t-90) cc_final: 0.6598 (t-170) REVERT: D 72 ILE cc_start: 0.8330 (tt) cc_final: 0.8031 (tt) REVERT: D 86 TYR cc_start: 0.8440 (m-10) cc_final: 0.6972 (m-10) REVERT: D 109 LEU cc_start: 0.8990 (tp) cc_final: 0.8410 (tp) REVERT: E 58 THR cc_start: 0.9150 (p) cc_final: 0.8891 (p) REVERT: E 64 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7855 (mtpt) REVERT: E 70 LEU cc_start: 0.8465 (mm) cc_final: 0.7936 (tp) REVERT: E 73 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7165 (mt-10) REVERT: F 29 ILE cc_start: 0.8385 (mm) cc_final: 0.8145 (mm) REVERT: F 88 TYR cc_start: 0.7692 (m-10) cc_final: 0.7208 (m-10) REVERT: F 95 ARG cc_start: 0.8246 (ptp-170) cc_final: 0.7970 (ptp90) REVERT: G 31 ILE cc_start: 0.8921 (tt) cc_final: 0.8588 (tp) REVERT: G 44 ARG cc_start: 0.7095 (tpt170) cc_final: 0.6792 (tpt170) REVERT: G 52 TYR cc_start: 0.6877 (t80) cc_final: 0.6571 (t80) REVERT: G 66 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6861 (tm-30) REVERT: G 67 LEU cc_start: 0.8330 (mt) cc_final: 0.8012 (mt) REVERT: G 81 THR cc_start: 0.8444 (m) cc_final: 0.8133 (p) REVERT: G 87 LEU cc_start: 0.6932 (tp) cc_final: 0.6019 (tp) REVERT: H 89 LYS cc_start: 0.8656 (tppp) cc_final: 0.8439 (mmmt) REVERT: H 92 ILE cc_start: 0.8841 (mt) cc_final: 0.8625 (mt) REVERT: K 199 ASP cc_start: 0.8209 (p0) cc_final: 0.6931 (p0) REVERT: K 231 ASP cc_start: 0.6881 (p0) cc_final: 0.6265 (p0) REVERT: K 236 PHE cc_start: 0.6102 (m-80) cc_final: 0.5880 (m-10) REVERT: K 250 ASN cc_start: 0.7934 (p0) cc_final: 0.7641 (p0) REVERT: K 269 ASP cc_start: 0.8263 (m-30) cc_final: 0.8020 (m-30) REVERT: K 305 ILE cc_start: 0.8821 (tt) cc_final: 0.8539 (pt) REVERT: K 310 GLN cc_start: 0.6746 (pp30) cc_final: 0.6463 (pp30) REVERT: K 323 PHE cc_start: 0.7646 (t80) cc_final: 0.7352 (t80) REVERT: K 330 LYS cc_start: 0.7150 (pptt) cc_final: 0.6755 (pptt) REVERT: K 331 GLU cc_start: 0.7294 (pm20) cc_final: 0.6017 (pm20) REVERT: K 352 TYR cc_start: 0.7810 (t80) cc_final: 0.7419 (t80) REVERT: K 356 THR cc_start: 0.8812 (m) cc_final: 0.8480 (m) REVERT: K 364 HIS cc_start: 0.7391 (t70) cc_final: 0.7121 (t70) REVERT: K 406 ASN cc_start: 0.8017 (p0) cc_final: 0.7787 (p0) REVERT: M 141 PHE cc_start: 0.8136 (p90) cc_final: 0.7856 (p90) REVERT: M 209 MET cc_start: 0.6498 (ttp) cc_final: 0.6063 (ttp) REVERT: M 353 LYS cc_start: 0.9072 (mptt) cc_final: 0.8791 (mptt) REVERT: N 8 GLU cc_start: 0.8381 (mp0) cc_final: 0.8038 (mp0) outliers start: 4 outliers final: 1 residues processed: 535 average time/residue: 0.1665 time to fit residues: 121.4231 Evaluate side-chains 481 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 480 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS ** D 66 ASN ** 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** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 GLN N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.105965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089430 restraints weight = 59113.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091449 restraints weight = 34691.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092773 restraints weight = 23649.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093628 restraints weight = 18157.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094142 restraints weight = 15274.702| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18310 Z= 0.174 Angle : 0.733 10.879 25948 Z= 0.404 Chirality : 0.041 0.204 2924 Planarity : 0.005 0.073 2268 Dihedral : 28.823 88.245 4818 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % 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 aren not related in a simple way. whole: -2.06 (0.22), residues: 1373 helix: -0.66 (0.19), residues: 712 sheet: -2.75 (1.02), residues: 26 loop : -2.13 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 428 TYR 0.023 0.002 TYR M 276 PHE 0.034 0.002 PHE N 21 TRP 0.041 0.003 TRP K 353 HIS 0.006 0.001 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00388 (18310) covalent geometry : angle 0.73347 (25948) hydrogen bonds : bond 0.04726 ( 821) hydrogen bonds : angle 4.24615 ( 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 520 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 518 time to evaluate : 0.419 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 58 THR cc_start: 0.8635 (p) cc_final: 0.8378 (t) REVERT: A 69 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8022 (ttp-110) REVERT: A 73 GLU cc_start: 0.7357 (pt0) cc_final: 0.7118 (pt0) REVERT: A 93 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 106 ASP cc_start: 0.7161 (m-30) cc_final: 0.6220 (m-30) REVERT: A 128 ARG cc_start: 0.8987 (mmm-85) cc_final: 0.8473 (mmm-85) REVERT: B 52 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 53 GLU cc_start: 0.7363 (pp20) cc_final: 0.7145 (pp20) REVERT: B 55 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8336 (mtp85) REVERT: C 52 TYR cc_start: 0.6172 (t80) cc_final: 0.5907 (t80) REVERT: C 63 GLU cc_start: 0.7718 (pp20) cc_final: 0.6902 (tm-30) REVERT: D 86 TYR cc_start: 0.8387 (m-10) cc_final: 0.6985 (m-10) REVERT: D 109 LEU cc_start: 0.8978 (tp) cc_final: 0.8406 (tp) REVERT: E 58 THR cc_start: 0.9234 (p) cc_final: 0.9013 (p) REVERT: E 64 LYS cc_start: 0.8265 (mtpp) cc_final: 0.8054 (mtpt) REVERT: E 76 GLN cc_start: 0.7338 (tp40) cc_final: 0.6773 (tp40) REVERT: F 29 ILE cc_start: 0.8318 (mm) cc_final: 0.8067 (mm) REVERT: F 50 ILE cc_start: 0.8578 (tp) cc_final: 0.8298 (tp) REVERT: F 88 TYR cc_start: 0.7548 (m-10) cc_final: 0.7000 (m-10) REVERT: F 95 ARG cc_start: 0.8319 (ptp-170) cc_final: 0.8072 (ptp90) REVERT: G 31 ILE cc_start: 0.8907 (tt) cc_final: 0.8608 (tp) REVERT: G 44 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6763 (tpt170) REVERT: G 66 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6830 (tm-30) REVERT: G 67 LEU cc_start: 0.8389 (mt) cc_final: 0.8189 (mt) REVERT: G 81 THR cc_start: 0.8509 (m) cc_final: 0.8231 (p) REVERT: G 87 LEU cc_start: 0.6936 (tp) cc_final: 0.6614 (tp) REVERT: H 38 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7261 (tm-30) REVERT: H 39 THR cc_start: 0.8036 (t) cc_final: 0.7693 (m) REVERT: H 43 TYR cc_start: 0.5349 (m-80) cc_final: 0.5149 (m-10) REVERT: H 89 LYS cc_start: 0.8592 (tppp) cc_final: 0.8300 (mmmt) REVERT: K 199 ASP cc_start: 0.8043 (p0) cc_final: 0.7801 (p0) REVERT: K 221 ARG cc_start: 0.6091 (ttt180) cc_final: 0.5759 (ttt180) REVERT: K 250 ASN cc_start: 0.8003 (p0) cc_final: 0.7756 (p0) REVERT: K 269 ASP cc_start: 0.8261 (m-30) cc_final: 0.8030 (m-30) REVERT: K 305 ILE cc_start: 0.8817 (tt) cc_final: 0.8524 (pt) REVERT: K 310 GLN cc_start: 0.7049 (pp30) cc_final: 0.6701 (pp30) REVERT: K 323 PHE cc_start: 0.7897 (t80) cc_final: 0.7553 (t80) REVERT: K 353 TRP cc_start: 0.8466 (m-90) cc_final: 0.7968 (m-90) REVERT: K 355 ASP cc_start: 0.8476 (p0) cc_final: 0.8122 (p0) REVERT: K 356 THR cc_start: 0.8849 (m) cc_final: 0.8546 (m) REVERT: K 383 ASP cc_start: 0.7848 (m-30) cc_final: 0.7547 (m-30) REVERT: M 141 PHE cc_start: 0.8211 (p90) cc_final: 0.7868 (p90) REVERT: M 192 LEU cc_start: 0.8374 (tp) cc_final: 0.8150 (tp) REVERT: M 209 MET cc_start: 0.6488 (ttp) cc_final: 0.6029 (ttp) REVERT: M 249 PHE cc_start: 0.6432 (t80) cc_final: 0.5762 (t80) REVERT: M 254 ASP cc_start: 0.8503 (p0) cc_final: 0.8202 (p0) REVERT: M 353 LYS cc_start: 0.9040 (mptt) cc_final: 0.8769 (mptt) REVERT: M 355 GLU cc_start: 0.7691 (pt0) cc_final: 0.7066 (pt0) REVERT: N 7 LEU cc_start: 0.8328 (pp) cc_final: 0.8091 (pp) REVERT: N 8 GLU cc_start: 0.8385 (mp0) cc_final: 0.7826 (mp0) REVERT: N 23 TYR cc_start: 0.7848 (t80) cc_final: 0.7614 (t80) outliers start: 2 outliers final: 1 residues processed: 520 average time/residue: 0.1612 time to fit residues: 114.6925 Evaluate side-chains 478 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 2.9990 chunk 96 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.106584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089841 restraints weight = 59173.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092075 restraints weight = 33318.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093510 restraints weight = 22058.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094452 restraints weight = 16623.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095045 restraints weight = 13715.190| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18310 Z= 0.170 Angle : 0.737 11.880 25948 Z= 0.406 Chirality : 0.041 0.207 2924 Planarity : 0.005 0.086 2268 Dihedral : 28.723 88.076 4818 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.08 % Allowed : 2.73 % Favored : 97.19 % 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 aren not related in a simple way. whole: -1.89 (0.22), residues: 1373 helix: -0.52 (0.19), residues: 700 sheet: -2.91 (0.99), residues: 26 loop : -1.99 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 78 TYR 0.023 0.002 TYR M 276 PHE 0.038 0.002 PHE K 236 TRP 0.028 0.002 TRP K 353 HIS 0.008 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00377 (18310) covalent geometry : angle 0.73679 (25948) hydrogen bonds : bond 0.04550 ( 821) hydrogen bonds : angle 4.25143 ( 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 523 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 522 time to evaluate : 0.519 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 58 THR cc_start: 0.8852 (p) cc_final: 0.8451 (t) REVERT: A 69 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8030 (ttp-110) REVERT: A 97 GLU cc_start: 0.7675 (tp30) cc_final: 0.7405 (mm-30) REVERT: A 106 ASP cc_start: 0.6963 (m-30) cc_final: 0.6258 (m-30) REVERT: B 37 LEU cc_start: 0.8946 (mt) cc_final: 0.8696 (mt) REVERT: B 44 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8006 (ptpp) REVERT: B 53 GLU cc_start: 0.7350 (pp20) cc_final: 0.6931 (pp20) REVERT: C 52 TYR cc_start: 0.6144 (t80) cc_final: 0.5695 (t80) REVERT: D 86 TYR cc_start: 0.8403 (m-10) cc_final: 0.7241 (m-10) REVERT: D 109 LEU cc_start: 0.9000 (tp) cc_final: 0.8385 (tp) REVERT: E 54 PHE cc_start: 0.7965 (m-10) cc_final: 0.7697 (m-10) REVERT: E 72 ARG cc_start: 0.8928 (mmt90) cc_final: 0.8665 (mmt-90) REVERT: E 73 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6403 (mt-10) REVERT: E 76 GLN cc_start: 0.7343 (tp40) cc_final: 0.6774 (tp40) REVERT: E 122 LYS cc_start: 0.7957 (tptp) cc_final: 0.7670 (mmmm) REVERT: E 125 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8124 (pttp) REVERT: E 129 ARG cc_start: 0.8472 (tpt90) cc_final: 0.8177 (tpt90) REVERT: F 29 ILE cc_start: 0.8390 (mm) cc_final: 0.8175 (mm) REVERT: F 82 THR cc_start: 0.8845 (t) cc_final: 0.8582 (t) REVERT: F 88 TYR cc_start: 0.7630 (m-10) cc_final: 0.7127 (m-10) REVERT: F 95 ARG cc_start: 0.8375 (ptp-170) cc_final: 0.8103 (ptp90) REVERT: G 30 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7108 (ttp-170) REVERT: G 66 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6693 (tm-30) REVERT: G 67 LEU cc_start: 0.8310 (mt) cc_final: 0.8013 (mt) REVERT: G 70 ASN cc_start: 0.7769 (p0) cc_final: 0.7497 (p0) REVERT: G 78 LYS cc_start: 0.7461 (mttp) cc_final: 0.7206 (mttt) REVERT: G 81 THR cc_start: 0.8326 (m) cc_final: 0.8083 (p) REVERT: G 87 LEU cc_start: 0.7063 (tp) cc_final: 0.6666 (tp) REVERT: G 93 ASP cc_start: 0.6721 (m-30) cc_final: 0.6510 (m-30) REVERT: H 89 LYS cc_start: 0.8330 (tppp) cc_final: 0.8085 (mmtt) REVERT: H 98 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7260 (tp40) REVERT: K 250 ASN cc_start: 0.7946 (p0) cc_final: 0.7630 (p0) REVERT: K 269 ASP cc_start: 0.8224 (m-30) cc_final: 0.7985 (m-30) REVERT: K 305 ILE cc_start: 0.8828 (tt) cc_final: 0.8586 (pt) REVERT: K 310 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6333 (pp30) REVERT: K 323 PHE cc_start: 0.7978 (t80) cc_final: 0.7776 (t80) REVERT: K 330 LYS cc_start: 0.7240 (pptt) cc_final: 0.6916 (pptt) REVERT: K 353 TRP cc_start: 0.8396 (m-90) cc_final: 0.7959 (m-90) REVERT: K 355 ASP cc_start: 0.8528 (p0) cc_final: 0.8196 (p0) REVERT: K 356 THR cc_start: 0.9093 (m) cc_final: 0.8562 (m) REVERT: K 364 HIS cc_start: 0.7246 (t70) cc_final: 0.7023 (t70) REVERT: K 368 ILE cc_start: 0.8299 (pt) cc_final: 0.7784 (pt) REVERT: K 383 ASP cc_start: 0.7838 (m-30) cc_final: 0.7552 (m-30) REVERT: K 428 ARG cc_start: 0.5553 (mtt90) cc_final: 0.5092 (ptp90) REVERT: L 28 THR cc_start: 0.8265 (p) cc_final: 0.8041 (p) REVERT: M 209 MET cc_start: 0.6380 (ttp) cc_final: 0.5922 (ttp) REVERT: M 249 PHE cc_start: 0.6366 (t80) cc_final: 0.5728 (t80) REVERT: M 254 ASP cc_start: 0.8466 (p0) cc_final: 0.8180 (p0) REVERT: M 353 LYS cc_start: 0.9040 (mptt) cc_final: 0.8728 (mptt) REVERT: M 355 GLU cc_start: 0.7630 (pt0) cc_final: 0.7008 (pt0) REVERT: N 7 LEU cc_start: 0.8352 (pp) cc_final: 0.8070 (pp) REVERT: N 8 GLU cc_start: 0.8403 (mp0) cc_final: 0.7850 (mp0) REVERT: N 23 TYR cc_start: 0.7909 (t80) cc_final: 0.7695 (t80) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.1580 time to fit residues: 112.6223 Evaluate side-chains 476 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 0.6980 chunk 70 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 140 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN N 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.107317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090547 restraints weight = 59293.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092774 restraints weight = 33363.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094190 restraints weight = 22073.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095105 restraints weight = 16614.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095691 restraints weight = 13744.625| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.8244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18310 Z= 0.167 Angle : 0.730 11.825 25948 Z= 0.402 Chirality : 0.041 0.171 2924 Planarity : 0.006 0.079 2268 Dihedral : 28.625 88.003 4818 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.08 % Allowed : 1.77 % Favored : 98.15 % 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 aren not related in a simple way. whole: -1.92 (0.22), residues: 1373 helix: -0.52 (0.19), residues: 713 sheet: -2.75 (0.91), residues: 26 loop : -2.08 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 78 TYR 0.027 0.002 TYR M 278 PHE 0.039 0.002 PHE D 73 TRP 0.024 0.002 TRP K 353 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00371 (18310) covalent geometry : angle 0.73021 (25948) hydrogen bonds : bond 0.04455 ( 821) hydrogen bonds : angle 4.27610 ( 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 515 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8382 (ttp80) cc_final: 0.7794 (ttp80) REVERT: A 58 THR cc_start: 0.8910 (p) cc_final: 0.8563 (t) REVERT: A 69 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8158 (ttp-110) REVERT: B 35 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8573 (ttt90) REVERT: B 44 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8299 (pttm) REVERT: C 44 ARG cc_start: 0.7502 (pmt-80) cc_final: 0.7220 (pmt-80) REVERT: C 52 TYR cc_start: 0.6033 (t80) cc_final: 0.5498 (t80) REVERT: D 46 LYS cc_start: 0.8317 (mmpt) cc_final: 0.8104 (mmpt) REVERT: D 73 PHE cc_start: 0.7820 (t80) cc_final: 0.7428 (t80) REVERT: D 76 ILE cc_start: 0.8750 (pt) cc_final: 0.8482 (pt) REVERT: D 86 TYR cc_start: 0.8417 (m-10) cc_final: 0.6972 (m-10) REVERT: D 102 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7719 (ttm110) REVERT: D 109 LEU cc_start: 0.8968 (tp) cc_final: 0.8371 (tp) REVERT: E 73 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6971 (mt-10) REVERT: E 76 GLN cc_start: 0.7275 (tp40) cc_final: 0.6846 (tp40) REVERT: E 125 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8021 (ptpp) REVERT: E 129 ARG cc_start: 0.8434 (tpt90) cc_final: 0.8063 (tpt90) REVERT: F 32 PRO cc_start: 0.4452 (Cg_exo) cc_final: 0.3799 (Cg_endo) REVERT: F 50 ILE cc_start: 0.8671 (tp) cc_final: 0.8366 (tp) REVERT: F 88 TYR cc_start: 0.7611 (m-10) cc_final: 0.7010 (m-10) REVERT: F 95 ARG cc_start: 0.8377 (ptp-170) cc_final: 0.7913 (ptp-170) REVERT: G 30 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7170 (ttm170) REVERT: G 44 ARG cc_start: 0.6914 (tpt90) cc_final: 0.6437 (tpt90) REVERT: G 52 TYR cc_start: 0.7019 (t80) cc_final: 0.6758 (t80) REVERT: G 67 LEU cc_start: 0.8367 (mt) cc_final: 0.8128 (mt) REVERT: G 81 THR cc_start: 0.8354 (m) cc_final: 0.8109 (p) REVERT: H 89 LYS cc_start: 0.8177 (tppp) cc_final: 0.7907 (mmtt) REVERT: H 98 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7236 (tp40) REVERT: H 99 THR cc_start: 0.8617 (p) cc_final: 0.8301 (t) REVERT: K 199 ASP cc_start: 0.8235 (p0) cc_final: 0.7889 (p0) REVERT: K 230 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6538 (mtm180) REVERT: K 250 ASN cc_start: 0.7962 (p0) cc_final: 0.7611 (p0) REVERT: K 305 ILE cc_start: 0.8821 (tt) cc_final: 0.8494 (pt) REVERT: K 323 PHE cc_start: 0.8191 (t80) cc_final: 0.7692 (t80) REVERT: K 330 LYS cc_start: 0.7257 (pptt) cc_final: 0.6977 (pptt) REVERT: K 331 GLU cc_start: 0.7148 (pm20) cc_final: 0.6668 (pm20) REVERT: K 353 TRP cc_start: 0.8499 (m-90) cc_final: 0.8013 (m-90) REVERT: K 355 ASP cc_start: 0.8506 (p0) cc_final: 0.8125 (p0) REVERT: K 356 THR cc_start: 0.9098 (m) cc_final: 0.8573 (m) REVERT: K 364 HIS cc_start: 0.7253 (t70) cc_final: 0.7048 (t70) REVERT: K 383 ASP cc_start: 0.7727 (m-30) cc_final: 0.7442 (m-30) REVERT: K 428 ARG cc_start: 0.5322 (mtt90) cc_final: 0.4770 (ptp90) REVERT: M 141 PHE cc_start: 0.7733 (p90) cc_final: 0.7430 (p90) REVERT: M 192 LEU cc_start: 0.8502 (pp) cc_final: 0.8209 (pp) REVERT: M 209 MET cc_start: 0.6331 (ttp) cc_final: 0.5889 (ttp) REVERT: M 249 PHE cc_start: 0.6253 (t80) cc_final: 0.5611 (t80) REVERT: M 254 ASP cc_start: 0.8378 (p0) cc_final: 0.8153 (p0) REVERT: M 353 LYS cc_start: 0.9012 (mptt) cc_final: 0.8726 (mptt) REVERT: M 355 GLU cc_start: 0.7558 (pt0) cc_final: 0.7006 (pt0) REVERT: N 7 LEU cc_start: 0.8348 (pp) cc_final: 0.8017 (pp) REVERT: N 8 GLU cc_start: 0.8357 (mp0) cc_final: 0.7828 (mp0) REVERT: N 23 TYR cc_start: 0.7890 (t80) cc_final: 0.7640 (t80) outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.1609 time to fit residues: 113.0459 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 : 0.498 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.105997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089333 restraints weight = 59687.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091551 restraints weight = 33683.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092975 restraints weight = 22352.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093917 restraints weight = 16821.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094490 restraints weight = 13877.779| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.8444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18310 Z= 0.188 Angle : 0.758 11.334 25948 Z= 0.413 Chirality : 0.041 0.245 2924 Planarity : 0.006 0.082 2268 Dihedral : 28.603 88.887 4818 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.16 % Allowed : 1.44 % 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 aren not related in a simple way. whole: -1.91 (0.22), residues: 1373 helix: -0.49 (0.19), residues: 702 sheet: -2.47 (0.99), residues: 26 loop : -2.10 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 83 TYR 0.022 0.002 TYR M 276 PHE 0.035 0.002 PHE K 236 TRP 0.022 0.002 TRP K 353 HIS 0.005 0.001 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00430 (18310) covalent geometry : angle 0.75799 (25948) hydrogen bonds : bond 0.04716 ( 821) hydrogen bonds : angle 4.28108 ( 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 496 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 494 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9020 (p) cc_final: 0.8649 (t) REVERT: A 69 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8177 (ttp-110) REVERT: B 35 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8528 (ttt90) REVERT: B 44 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8457 (pttm) REVERT: B 51 TYR cc_start: 0.8658 (m-80) cc_final: 0.8280 (m-10) REVERT: B 53 GLU cc_start: 0.7392 (pp20) cc_final: 0.7089 (pp20) REVERT: D 86 TYR cc_start: 0.8404 (m-10) cc_final: 0.7116 (m-10) REVERT: D 98 GLN cc_start: 0.7949 (tp40) cc_final: 0.7502 (tp40) REVERT: D 109 LEU cc_start: 0.9028 (tp) cc_final: 0.8458 (tp) REVERT: E 73 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6999 (mt-10) REVERT: E 74 ILE cc_start: 0.8722 (pt) cc_final: 0.8458 (mm) REVERT: E 76 GLN cc_start: 0.7171 (tp40) cc_final: 0.6425 (tp40) REVERT: E 97 GLU cc_start: 0.7931 (pm20) cc_final: 0.7702 (pm20) REVERT: E 121 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8249 (ttpp) REVERT: E 125 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7671 (pttp) REVERT: E 129 ARG cc_start: 0.8502 (tpt90) cc_final: 0.8264 (tpt90) REVERT: F 50 ILE cc_start: 0.8726 (tp) cc_final: 0.8522 (tp) REVERT: F 88 TYR cc_start: 0.7609 (m-10) cc_final: 0.7040 (m-10) REVERT: G 30 ARG cc_start: 0.7569 (ttm170) cc_final: 0.7265 (ttp-170) REVERT: G 31 ILE cc_start: 0.8872 (tt) cc_final: 0.8527 (tp) REVERT: G 44 ARG cc_start: 0.7055 (tpt90) cc_final: 0.6484 (tpt90) REVERT: G 67 LEU cc_start: 0.8418 (mt) cc_final: 0.8210 (mt) REVERT: G 70 ASN cc_start: 0.7501 (p0) cc_final: 0.7291 (p0) REVERT: G 81 THR cc_start: 0.8396 (m) cc_final: 0.8124 (p) REVERT: H 37 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7420 (ttpp) REVERT: H 89 LYS cc_start: 0.8341 (tppp) cc_final: 0.7812 (mmtt) REVERT: H 98 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7261 (tp40) REVERT: H 99 THR cc_start: 0.8524 (p) cc_final: 0.8206 (t) REVERT: K 250 ASN cc_start: 0.7989 (p0) cc_final: 0.7730 (p0) REVERT: K 305 ILE cc_start: 0.8875 (tt) cc_final: 0.8533 (pt) REVERT: K 323 PHE cc_start: 0.8324 (t80) cc_final: 0.7779 (t80) REVERT: K 330 LYS cc_start: 0.7345 (pptt) cc_final: 0.6999 (pptt) REVERT: K 353 TRP cc_start: 0.8449 (m-90) cc_final: 0.7953 (m-90) REVERT: K 355 ASP cc_start: 0.8466 (p0) cc_final: 0.8166 (p0) REVERT: K 356 THR cc_start: 0.9092 (m) cc_final: 0.8625 (m) REVERT: K 364 HIS cc_start: 0.7289 (t70) cc_final: 0.7053 (t70) REVERT: K 383 ASP cc_start: 0.7687 (m-30) cc_final: 0.7403 (m-30) REVERT: M 141 PHE cc_start: 0.7874 (p90) cc_final: 0.7312 (p90) REVERT: M 192 LEU cc_start: 0.8690 (pp) cc_final: 0.8249 (pt) REVERT: M 209 MET cc_start: 0.6488 (ttp) cc_final: 0.6029 (ttp) REVERT: M 249 PHE cc_start: 0.6216 (t80) cc_final: 0.5619 (t80) REVERT: M 254 ASP cc_start: 0.8387 (p0) cc_final: 0.8153 (p0) REVERT: M 259 MET cc_start: 0.4381 (pmm) cc_final: 0.4154 (pmm) REVERT: M 280 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7552 (mmt180) REVERT: M 353 LYS cc_start: 0.9007 (mptt) cc_final: 0.8711 (mptt) REVERT: M 355 GLU cc_start: 0.7583 (pt0) cc_final: 0.7086 (pt0) REVERT: N 7 LEU cc_start: 0.8281 (pp) cc_final: 0.8004 (pp) REVERT: N 8 GLU cc_start: 0.8385 (mp0) cc_final: 0.7796 (mp0) REVERT: N 23 TYR cc_start: 0.7877 (t80) cc_final: 0.7624 (t80) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.1628 time to fit residues: 110.0685 Evaluate side-chains 453 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 0.0870 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN H 87 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.106755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090415 restraints weight = 58924.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092393 restraints weight = 34631.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093697 restraints weight = 23715.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094545 restraints weight = 18216.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095096 restraints weight = 15292.102| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.8637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18310 Z= 0.175 Angle : 0.762 11.905 25948 Z= 0.416 Chirality : 0.041 0.231 2924 Planarity : 0.006 0.082 2268 Dihedral : 28.584 88.547 4818 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.08 % Allowed : 0.64 % Favored : 99.28 % 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 aren not related in a simple way. whole: -1.89 (0.22), residues: 1373 helix: -0.50 (0.20), residues: 701 sheet: -2.50 (1.04), residues: 26 loop : -2.06 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 83 TYR 0.021 0.002 TYR H 43 PHE 0.029 0.002 PHE N 21 TRP 0.026 0.002 TRP K 247 HIS 0.006 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00393 (18310) covalent geometry : angle 0.76248 (25948) hydrogen bonds : bond 0.04547 ( 821) hydrogen bonds : angle 4.29923 ( 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 500 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 0.520 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 57 SER cc_start: 0.8596 (p) cc_final: 0.8099 (p) REVERT: A 58 THR cc_start: 0.9061 (p) cc_final: 0.8584 (t) REVERT: A 59 GLU cc_start: 0.8182 (pm20) cc_final: 0.7875 (pm20) REVERT: A 69 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8138 (ttp-110) REVERT: B 35 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8430 (ttt90) REVERT: B 44 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8435 (pttp) REVERT: D 86 TYR cc_start: 0.8390 (m-10) cc_final: 0.7052 (m-10) REVERT: D 102 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7876 (ttm110) REVERT: D 109 LEU cc_start: 0.9020 (tp) cc_final: 0.8461 (tp) REVERT: E 56 LYS cc_start: 0.9153 (tttp) cc_final: 0.8378 (tptp) REVERT: E 73 GLU cc_start: 0.7837 (mt-10) cc_final: 0.6907 (mt-10) REVERT: E 76 GLN cc_start: 0.7350 (tp40) cc_final: 0.6928 (tp40) REVERT: E 121 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8205 (ttpp) REVERT: E 125 LYS cc_start: 0.8439 (ptpp) cc_final: 0.7678 (pttp) REVERT: E 129 ARG cc_start: 0.8512 (tpt90) cc_final: 0.8206 (tpt90) REVERT: F 49 LEU cc_start: 0.8042 (tt) cc_final: 0.7646 (tp) REVERT: F 50 ILE cc_start: 0.8699 (tp) cc_final: 0.8373 (tp) REVERT: F 59 LYS cc_start: 0.8848 (tppt) cc_final: 0.8525 (mptt) REVERT: F 88 TYR cc_start: 0.7612 (m-10) cc_final: 0.7109 (m-10) REVERT: F 95 ARG cc_start: 0.8382 (ptp-170) cc_final: 0.8169 (ptp90) REVERT: G 67 LEU cc_start: 0.8441 (mt) cc_final: 0.8238 (mt) REVERT: G 70 ASN cc_start: 0.7472 (p0) cc_final: 0.7258 (p0) REVERT: G 81 THR cc_start: 0.8432 (m) cc_final: 0.8104 (p) REVERT: H 37 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7416 (ttpp) REVERT: H 89 LYS cc_start: 0.8126 (tppp) cc_final: 0.7668 (mmtt) REVERT: K 199 ASP cc_start: 0.8087 (p0) cc_final: 0.7595 (p0) REVERT: K 214 TYR cc_start: 0.8489 (t80) cc_final: 0.8201 (t80) REVERT: K 250 ASN cc_start: 0.8007 (p0) cc_final: 0.7660 (p0) REVERT: K 251 LEU cc_start: 0.8386 (mm) cc_final: 0.8100 (mp) REVERT: K 292 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7528 (mmmt) REVERT: K 305 ILE cc_start: 0.8867 (tt) cc_final: 0.8519 (pt) REVERT: K 330 LYS cc_start: 0.7068 (pptt) cc_final: 0.6843 (pptt) REVERT: K 331 GLU cc_start: 0.7179 (pm20) cc_final: 0.6622 (pm20) REVERT: K 353 TRP cc_start: 0.8554 (m-90) cc_final: 0.7876 (m-90) REVERT: K 355 ASP cc_start: 0.8386 (p0) cc_final: 0.8120 (p0) REVERT: K 356 THR cc_start: 0.9092 (m) cc_final: 0.8626 (m) REVERT: K 357 LEU cc_start: 0.8544 (mt) cc_final: 0.8309 (mt) REVERT: K 364 HIS cc_start: 0.7215 (t70) cc_final: 0.6991 (t70) REVERT: K 383 ASP cc_start: 0.7758 (m-30) cc_final: 0.7469 (m-30) REVERT: M 141 PHE cc_start: 0.7626 (p90) cc_final: 0.7151 (p90) REVERT: M 192 LEU cc_start: 0.8549 (pp) cc_final: 0.8063 (pt) REVERT: M 209 MET cc_start: 0.6464 (ttp) cc_final: 0.5997 (ttp) REVERT: M 224 LEU cc_start: 0.4944 (pt) cc_final: 0.4441 (pp) REVERT: M 249 PHE cc_start: 0.6069 (t80) cc_final: 0.5541 (t80) REVERT: M 254 ASP cc_start: 0.8334 (p0) cc_final: 0.8109 (p0) REVERT: M 259 MET cc_start: 0.4321 (pmm) cc_final: 0.4035 (pmm) REVERT: M 276 TYR cc_start: 0.4782 (t80) cc_final: 0.4313 (t80) REVERT: M 280 ARG cc_start: 0.7827 (mmt180) cc_final: 0.7576 (mpt180) REVERT: M 353 LYS cc_start: 0.9003 (mptt) cc_final: 0.8713 (mptt) REVERT: M 355 GLU cc_start: 0.7602 (pt0) cc_final: 0.7102 (pt0) REVERT: M 358 SER cc_start: 0.8899 (p) cc_final: 0.7807 (p) REVERT: M 361 TRP cc_start: 0.6032 (m-10) cc_final: 0.5751 (m-10) REVERT: N 7 LEU cc_start: 0.8336 (pp) cc_final: 0.8111 (pp) REVERT: N 8 GLU cc_start: 0.8379 (mp0) cc_final: 0.7772 (mp0) REVERT: N 23 TYR cc_start: 0.7907 (t80) cc_final: 0.7649 (t80) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.1556 time to fit residues: 107.0063 Evaluate side-chains 458 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 0.5980 chunk 87 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN F 93 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.107223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090807 restraints weight = 59693.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092817 restraints weight = 35141.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094120 restraints weight = 23980.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094987 restraints weight = 18465.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095532 restraints weight = 15487.753| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18310 Z= 0.173 Angle : 0.755 13.961 25948 Z= 0.413 Chirality : 0.041 0.261 2924 Planarity : 0.006 0.101 2268 Dihedral : 28.554 88.391 4818 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.16 % Allowed : 0.40 % 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 aren not related in a simple way. whole: -1.80 (0.22), residues: 1373 helix: -0.46 (0.20), residues: 695 sheet: -2.12 (1.03), residues: 26 loop : -1.97 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 78 TYR 0.050 0.002 TYR K 352 PHE 0.031 0.002 PHE K 237 TRP 0.027 0.002 TRP K 353 HIS 0.006 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00389 (18310) covalent geometry : angle 0.75464 (25948) hydrogen bonds : bond 0.04551 ( 821) hydrogen bonds : angle 4.30933 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.30 seconds wall clock time: 57 minutes 9.27 seconds (3429.27 seconds total)