Starting phenix.real_space_refine on Wed Jun 18 19:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2y_38022/06_2025/8x2y_38022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2y_38022/06_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_38022/06_2025/8x2y_38022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2y_38022/06_2025/8x2y_38022.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2y_38022/06_2025/8x2y_38022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2y_38022/06_2025/8x2y_38022.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.69, per 1000 atoms: 0.56 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: 3.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.77 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: 8.25 Time building geometry restraints manager: 4.80 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.610 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.003 TRP K 353 HIS 0.015 0.002 HIS B 75 PHE 0.019 0.002 PHE K 271 TYR 0.043 0.003 TYR F 98 ARG 0.009 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.17855 ( 821) hydrogen bonds : angle 7.17455 ( 2079) covalent geometry : bond 0.00623 (18310) covalent geometry : angle 0.99098 (25948) *********************** 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 : 1.496 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: 0.3826 time to fit residues: 291.2955 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 : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 GLN L 20 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS N 102 ASN N 107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089176 restraints weight = 58306.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091658 restraints weight = 30862.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093273 restraints weight = 19413.384| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18310 Z= 0.203 Angle : 0.770 11.125 25948 Z= 0.429 Chirality : 0.043 0.253 2924 Planarity : 0.006 0.052 2268 Dihedral : 29.350 89.657 4818 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.64 % Allowed : 5.54 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1373 helix: -1.74 (0.17), residues: 691 sheet: -2.35 (0.96), residues: 26 loop : -2.54 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 353 HIS 0.010 0.002 HIS M 338 PHE 0.023 0.002 PHE E 54 TYR 0.031 0.002 TYR F 98 ARG 0.011 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.05316 ( 821) hydrogen bonds : angle 4.81752 ( 2079) covalent geometry : bond 0.00442 (18310) covalent geometry : angle 0.77017 (25948) *********************** 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 518 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 510 time to evaluate : 1.544 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: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8363 (mmmt) cc_final: 0.8147 (mmmt) REVERT: A 93 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7769 (tm-30) REVERT: A 125 LYS cc_start: 0.8511 (tppt) cc_final: 0.8017 (tppt) REVERT: B 37 LEU cc_start: 0.8865 (tp) cc_final: 0.8520 (tp) REVERT: C 63 GLU cc_start: 0.7833 (pp20) cc_final: 0.7489 (tm-30) REVERT: C 84 HIS cc_start: 0.6732 (t-90) cc_final: 0.6139 (t-170) REVERT: D 42 SER cc_start: 0.8607 (m) cc_final: 0.8262 (p) REVERT: D 51 THR cc_start: 0.7909 (p) cc_final: 0.7669 (p) REVERT: D 57 ILE cc_start: 0.7575 (mm) cc_final: 0.7137 (tp) REVERT: D 71 ASP cc_start: 0.7515 (m-30) cc_final: 0.7234 (m-30) REVERT: D 88 LYS cc_start: 0.8324 (mmmm) cc_final: 0.8073 (mmmm) REVERT: D 98 GLN cc_start: 0.7835 (tp40) cc_final: 0.7292 (tp40) REVERT: E 83 ARG cc_start: 0.7509 (tpm170) cc_final: 0.7225 (mmm160) REVERT: F 27 GLN cc_start: 0.7808 (mp-120) cc_final: 0.5944 (mp10) REVERT: F 49 LEU cc_start: 0.7151 (tt) cc_final: 0.6698 (tp) REVERT: F 63 GLU cc_start: 0.7076 (tp30) cc_final: 0.6141 (tp30) REVERT: F 78 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7411 (ptp90) REVERT: F 82 THR cc_start: 0.8047 (t) cc_final: 0.7069 (p) REVERT: F 88 TYR cc_start: 0.6625 (m-10) cc_final: 0.6297 (m-10) REVERT: G 67 LEU cc_start: 0.7693 (mt) cc_final: 0.7206 (mt) REVERT: G 81 THR cc_start: 0.8021 (m) cc_final: 0.7509 (p) REVERT: G 113 ASN cc_start: 0.9045 (t0) cc_final: 0.8807 (t0) REVERT: H 43 TYR cc_start: 0.5316 (m-80) cc_final: 0.5067 (m-10) REVERT: H 63 SER cc_start: 0.8244 (t) cc_final: 0.7652 (p) REVERT: H 65 LEU cc_start: 0.7963 (mm) cc_final: 0.7614 (mm) REVERT: H 74 GLU cc_start: 0.7509 (tp30) cc_final: 0.7272 (tp30) REVERT: K 167 LEU cc_start: 0.8592 (mm) cc_final: 0.8124 (tp) REVERT: K 251 LEU cc_start: 0.8103 (mt) cc_final: 0.7794 (mt) REVERT: K 269 ASP cc_start: 0.8609 (m-30) cc_final: 0.8317 (m-30) REVERT: K 274 TYR cc_start: 0.7406 (m-10) cc_final: 0.7200 (m-10) REVERT: K 364 HIS cc_start: 0.6710 (t-90) cc_final: 0.6395 (t-90) REVERT: K 406 ASN cc_start: 0.6173 (p0) cc_final: 0.5971 (p0) REVERT: L 40 GLU cc_start: 0.7042 (tm-30) cc_final: 0.5751 (tm-30) REVERT: L 44 PHE cc_start: 0.7510 (m-10) cc_final: 0.7093 (m-10) REVERT: M 141 PHE cc_start: 0.8040 (p90) cc_final: 0.7763 (p90) REVERT: M 166 GLU cc_start: 0.8239 (mp0) cc_final: 0.8031 (mp0) REVERT: M 234 LEU cc_start: 0.6850 (mt) cc_final: 0.6635 (mt) REVERT: N 8 GLU cc_start: 0.8320 (mp0) cc_final: 0.7940 (mp0) REVERT: N 31 ASN cc_start: 0.8362 (m110) cc_final: 0.7812 (t0) REVERT: N 96 LEU cc_start: 0.8382 (pp) cc_final: 0.8036 (pp) outliers start: 8 outliers final: 1 residues processed: 513 average time/residue: 0.4237 time to fit residues: 302.9961 Evaluate side-chains 447 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.106143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089394 restraints weight = 57903.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091799 restraints weight = 30838.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093353 restraints weight = 19473.666| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18310 Z= 0.184 Angle : 0.718 10.824 25948 Z= 0.403 Chirality : 0.041 0.165 2924 Planarity : 0.005 0.085 2268 Dihedral : 28.987 88.356 4818 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1373 helix: -1.18 (0.18), residues: 705 sheet: -1.88 (1.10), residues: 26 loop : -2.47 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 353 HIS 0.004 0.001 HIS H 52 PHE 0.021 0.002 PHE K 236 TYR 0.029 0.002 TYR F 98 ARG 0.006 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 821) hydrogen bonds : angle 4.41440 ( 2079) covalent geometry : bond 0.00395 (18310) covalent geometry : angle 0.71751 (25948) *********************** 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 502 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.442 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: 0.8463 (m-80) cc_final: 0.8258 (m-80) REVERT: A 125 LYS cc_start: 0.8671 (tppt) cc_final: 0.8164 (tppt) REVERT: A 131 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7478 (mmm-85) REVERT: B 67 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7386 (ttm-80) REVERT: C 63 GLU cc_start: 0.7913 (pp20) cc_final: 0.7407 (tm-30) REVERT: C 84 HIS cc_start: 0.6836 (t-90) cc_final: 0.6273 (t-170) REVERT: C 113 ASN cc_start: 0.7922 (p0) cc_final: 0.7576 (p0) REVERT: D 42 SER cc_start: 0.8535 (m) cc_final: 0.8307 (p) REVERT: D 57 ILE cc_start: 0.8039 (mm) cc_final: 0.7817 (tp) REVERT: D 68 PHE cc_start: 0.8324 (t80) cc_final: 0.7952 (t80) REVERT: D 96 GLU cc_start: 0.7622 (pt0) cc_final: 0.7387 (pt0) REVERT: D 98 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7512 (tp40) REVERT: D 102 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7676 (ttm110) REVERT: E 45 THR cc_start: 0.7712 (p) cc_final: 0.7076 (p) REVERT: E 48 LEU cc_start: 0.8074 (mt) cc_final: 0.7819 (mp) REVERT: E 50 GLU cc_start: 0.7369 (pp20) cc_final: 0.7138 (pp20) REVERT: E 60 LEU cc_start: 0.8931 (pp) cc_final: 0.8279 (pp) REVERT: E 70 LEU cc_start: 0.8518 (mm) cc_final: 0.8178 (tp) REVERT: F 71 THR cc_start: 0.8894 (m) cc_final: 0.8657 (t) REVERT: F 82 THR cc_start: 0.8390 (t) cc_final: 0.7515 (p) REVERT: F 88 TYR cc_start: 0.7079 (m-10) cc_final: 0.6658 (m-10) REVERT: G 24 LEU cc_start: 0.8344 (mt) cc_final: 0.8102 (mt) REVERT: G 67 LEU cc_start: 0.8066 (mt) cc_final: 0.7634 (mt) REVERT: G 81 THR cc_start: 0.8209 (m) cc_final: 0.7718 (p) REVERT: G 87 LEU cc_start: 0.7383 (tp) cc_final: 0.7006 (tp) REVERT: H 50 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7826 (tm-30) REVERT: H 74 GLU cc_start: 0.7579 (tp30) cc_final: 0.7141 (tp30) REVERT: K 176 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7433 (tp30) REVERT: K 238 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6038 (mt-10) REVERT: K 251 LEU cc_start: 0.8113 (mt) cc_final: 0.7719 (mp) REVERT: K 308 LEU cc_start: 0.8857 (tp) cc_final: 0.8567 (tp) REVERT: K 364 HIS cc_start: 0.7033 (t-90) cc_final: 0.6559 (t-90) REVERT: K 406 ASN cc_start: 0.6437 (p0) cc_final: 0.6231 (p0) REVERT: L 40 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6413 (tm-30) REVERT: L 44 PHE cc_start: 0.7304 (m-10) cc_final: 0.6746 (m-10) REVERT: M 209 MET cc_start: 0.5764 (ttp) cc_final: 0.5523 (ttp) REVERT: M 217 PHE cc_start: 0.7222 (t80) cc_final: 0.6909 (t80) REVERT: M 289 TYR cc_start: 0.6370 (m-80) cc_final: 0.6169 (m-80) REVERT: N 8 GLU cc_start: 0.8313 (mp0) cc_final: 0.7935 (mp0) REVERT: N 31 ASN cc_start: 0.8081 (m110) cc_final: 0.7565 (t0) REVERT: N 97 ILE cc_start: 0.8028 (mt) cc_final: 0.7748 (mt) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.4674 time to fit residues: 328.0254 Evaluate side-chains 451 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 123 optimal weight: 0.0020 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN H 87 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS K 312 GLN K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.106167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089335 restraints weight = 57882.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091703 restraints weight = 30907.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093240 restraints weight = 19605.038| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18310 Z= 0.179 Angle : 0.710 10.880 25948 Z= 0.396 Chirality : 0.041 0.183 2924 Planarity : 0.005 0.050 2268 Dihedral : 28.701 88.554 4818 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 1373 helix: -0.81 (0.18), residues: 698 sheet: -1.84 (1.15), residues: 26 loop : -2.34 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP K 353 HIS 0.005 0.001 HIS M 198 PHE 0.058 0.002 PHE N 21 TYR 0.025 0.002 TYR B 72 ARG 0.009 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 821) hydrogen bonds : angle 4.18388 ( 2079) covalent geometry : bond 0.00401 (18310) covalent geometry : angle 0.71010 (25948) *********************** 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 522 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.466 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: symmetry clash REVERT: A 65 LEU cc_start: 0.8475 (mm) cc_final: 0.8272 (mp) REVERT: A 69 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.8222 (ptp90) REVERT: A 82 LEU cc_start: 0.8674 (mt) cc_final: 0.8417 (mm) REVERT: A 93 GLN cc_start: 0.8220 (tp40) cc_final: 0.7984 (tm-30) REVERT: A 123 ASP cc_start: 0.7529 (m-30) cc_final: 0.7265 (t0) REVERT: A 125 LYS cc_start: 0.8645 (tppt) cc_final: 0.8219 (tppt) REVERT: A 130 LEU cc_start: 0.8469 (tt) cc_final: 0.8235 (tt) REVERT: C 63 GLU cc_start: 0.7946 (pp20) cc_final: 0.7330 (tm-30) REVERT: C 84 HIS cc_start: 0.7078 (t-90) cc_final: 0.6581 (t-170) REVERT: C 113 ASN cc_start: 0.7899 (p0) cc_final: 0.7657 (p0) REVERT: D 57 ILE cc_start: 0.8184 (mm) cc_final: 0.7920 (tp) REVERT: D 68 PHE cc_start: 0.8389 (t80) cc_final: 0.7575 (t80) REVERT: D 86 TYR cc_start: 0.8366 (m-10) cc_final: 0.7158 (m-10) REVERT: E 60 LEU cc_start: 0.8957 (pp) cc_final: 0.8165 (pp) REVERT: E 73 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6866 (mt-10) REVERT: E 121 LYS cc_start: 0.8368 (ptmm) cc_final: 0.8153 (ttpp) REVERT: F 58 LEU cc_start: 0.8665 (mt) cc_final: 0.8453 (mt) REVERT: F 62 LEU cc_start: 0.8244 (tt) cc_final: 0.8029 (tp) REVERT: F 63 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7276 (mm-30) REVERT: F 78 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7785 (ptp90) REVERT: F 82 THR cc_start: 0.8504 (t) cc_final: 0.7743 (p) REVERT: F 88 TYR cc_start: 0.7248 (m-10) cc_final: 0.6835 (m-10) REVERT: G 81 THR cc_start: 0.8425 (m) cc_final: 0.7878 (p) REVERT: G 87 LEU cc_start: 0.7427 (tp) cc_final: 0.6454 (tp) REVERT: H 50 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7986 (tm-30) REVERT: H 65 LEU cc_start: 0.8240 (mm) cc_final: 0.7866 (mt) REVERT: H 74 GLU cc_start: 0.7644 (tp30) cc_final: 0.7251 (tp30) REVERT: H 118 THR cc_start: 0.8658 (t) cc_final: 0.8412 (p) REVERT: K 231 ASP cc_start: 0.6210 (p0) cc_final: 0.5717 (p0) REVERT: K 251 LEU cc_start: 0.8176 (mt) cc_final: 0.7652 (mp) REVERT: K 356 THR cc_start: 0.8226 (m) cc_final: 0.7967 (m) REVERT: K 406 ASN cc_start: 0.7047 (p0) cc_final: 0.6792 (p0) REVERT: L 40 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7139 (tp30) REVERT: M 209 MET cc_start: 0.6006 (ttp) cc_final: 0.5633 (ttp) REVERT: M 217 PHE cc_start: 0.6985 (t80) cc_final: 0.6772 (t80) REVERT: M 234 LEU cc_start: 0.6869 (mt) cc_final: 0.6660 (mt) REVERT: N 7 LEU cc_start: 0.8382 (pp) cc_final: 0.8118 (pp) REVERT: N 8 GLU cc_start: 0.8390 (mp0) cc_final: 0.7856 (mp0) REVERT: N 89 LEU cc_start: 0.7173 (pp) cc_final: 0.6549 (mt) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3843 time to fit residues: 273.8494 Evaluate side-chains 463 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 93 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089675 restraints weight = 59337.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091938 restraints weight = 32286.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093423 restraints weight = 20830.566| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18310 Z= 0.178 Angle : 0.719 10.861 25948 Z= 0.399 Chirality : 0.042 0.450 2924 Planarity : 0.005 0.067 2268 Dihedral : 28.621 88.126 4818 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.21), residues: 1373 helix: -0.68 (0.19), residues: 712 sheet: -1.92 (1.10), residues: 26 loop : -2.33 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP K 353 HIS 0.005 0.001 HIS M 198 PHE 0.028 0.002 PHE K 236 TYR 0.025 0.002 TYR F 98 ARG 0.009 0.001 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 821) hydrogen bonds : angle 4.18667 ( 2079) covalent geometry : bond 0.00395 (18310) covalent geometry : angle 0.71933 (25948) *********************** 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 515 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 1.769 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: A 60 LEU cc_start: 0.8803 (mm) cc_final: 0.8276 (mt) REVERT: A 125 LYS cc_start: 0.8703 (tppt) cc_final: 0.8278 (tppt) REVERT: A 128 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8309 (mtp85) REVERT: B 59 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8465 (tppp) REVERT: B 67 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.7407 (ttm-80) REVERT: B 80 THR cc_start: 0.8115 (t) cc_final: 0.7833 (t) REVERT: C 52 TYR cc_start: 0.6020 (t80) cc_final: 0.5819 (t80) REVERT: C 74 ASP cc_start: 0.8104 (t0) cc_final: 0.7879 (t0) REVERT: D 57 ILE cc_start: 0.8366 (mm) cc_final: 0.7474 (tp) REVERT: D 71 ASP cc_start: 0.7532 (p0) cc_final: 0.6965 (p0) REVERT: D 73 PHE cc_start: 0.7956 (t80) cc_final: 0.7660 (t80) REVERT: D 74 GLU cc_start: 0.7746 (tp30) cc_final: 0.7496 (tp30) REVERT: D 102 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7631 (ttm110) REVERT: D 114 VAL cc_start: 0.8660 (t) cc_final: 0.8349 (p) REVERT: E 56 LYS cc_start: 0.8991 (tttp) cc_final: 0.8530 (tttp) REVERT: E 59 GLU cc_start: 0.7950 (tp30) cc_final: 0.7742 (tp30) REVERT: E 76 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7192 (tp40) REVERT: F 27 GLN cc_start: 0.8250 (pm20) cc_final: 0.7825 (pm20) REVERT: F 49 LEU cc_start: 0.8059 (tt) cc_final: 0.7766 (tt) REVERT: F 58 LEU cc_start: 0.8664 (mt) cc_final: 0.8457 (mt) REVERT: F 63 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6951 (tp30) REVERT: F 88 TYR cc_start: 0.7321 (m-10) cc_final: 0.6821 (m-10) REVERT: G 44 ARG cc_start: 0.7338 (tpt170) cc_final: 0.6988 (tpt170) REVERT: G 66 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6678 (tm-30) REVERT: G 67 LEU cc_start: 0.8347 (mt) cc_final: 0.8095 (mt) REVERT: G 87 LEU cc_start: 0.7146 (tp) cc_final: 0.6527 (tp) REVERT: G 94 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6948 (mm-30) REVERT: H 74 GLU cc_start: 0.7534 (tp30) cc_final: 0.7321 (tp30) REVERT: H 118 THR cc_start: 0.8622 (t) cc_final: 0.8408 (p) REVERT: K 170 ILE cc_start: 0.8739 (mt) cc_final: 0.8510 (pt) REVERT: K 251 LEU cc_start: 0.8260 (mt) cc_final: 0.7813 (mt) REVERT: K 292 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7182 (mmmt) REVERT: K 356 THR cc_start: 0.8645 (m) cc_final: 0.8111 (m) REVERT: K 357 LEU cc_start: 0.8420 (mt) cc_final: 0.8069 (mt) REVERT: K 364 HIS cc_start: 0.7104 (t70) cc_final: 0.6871 (t70) REVERT: K 381 THR cc_start: 0.8915 (m) cc_final: 0.8496 (t) REVERT: K 406 ASN cc_start: 0.7380 (p0) cc_final: 0.7099 (p0) REVERT: L 40 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6341 (tm-30) REVERT: L 44 PHE cc_start: 0.7609 (m-10) cc_final: 0.6840 (m-10) REVERT: M 209 MET cc_start: 0.6121 (ttp) cc_final: 0.5805 (ttp) REVERT: M 350 LEU cc_start: 0.9087 (tp) cc_final: 0.8886 (tp) REVERT: N 7 LEU cc_start: 0.8331 (pp) cc_final: 0.7985 (pp) REVERT: N 8 GLU cc_start: 0.8359 (mp0) cc_final: 0.7828 (mp0) REVERT: N 26 GLU cc_start: 0.7650 (tt0) cc_final: 0.7364 (tt0) REVERT: N 89 LEU cc_start: 0.7117 (pp) cc_final: 0.6543 (mt) REVERT: N 97 ILE cc_start: 0.8260 (mt) cc_final: 0.8060 (mt) outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.4122 time to fit residues: 291.8920 Evaluate side-chains 465 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 102 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 93 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.106395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090067 restraints weight = 59084.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092351 restraints weight = 32391.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093830 restraints weight = 20904.124| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6579 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= 0.171 Angle : 0.711 11.072 25948 Z= 0.395 Chirality : 0.040 0.184 2924 Planarity : 0.005 0.082 2268 Dihedral : 28.580 88.047 4818 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.22), residues: 1373 helix: -0.56 (0.19), residues: 708 sheet: -1.53 (1.05), residues: 26 loop : -2.19 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 353 HIS 0.006 0.001 HIS H 112 PHE 0.036 0.002 PHE N 21 TYR 0.022 0.002 TYR F 98 ARG 0.014 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 821) hydrogen bonds : angle 4.16595 ( 2079) covalent geometry : bond 0.00382 (18310) covalent geometry : angle 0.71077 (25948) *********************** 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 508 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 1.364 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: A 46 VAL cc_start: 0.8252 (p) cc_final: 0.7807 (p) REVERT: A 49 ARG cc_start: 0.7439 (mtp180) cc_final: 0.7175 (mtp180) REVERT: A 50 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: A 125 LYS cc_start: 0.8689 (tppt) cc_final: 0.8264 (tppt) REVERT: B 59 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8551 (tppp) REVERT: C 36 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7573 (mmmm) REVERT: C 52 TYR cc_start: 0.5805 (t80) cc_final: 0.5526 (t80) REVERT: C 84 HIS cc_start: 0.7471 (t-170) cc_final: 0.7241 (t70) REVERT: D 71 ASP cc_start: 0.7461 (p0) cc_final: 0.6857 (p0) REVERT: D 73 PHE cc_start: 0.7919 (t80) cc_final: 0.7599 (t80) REVERT: D 76 ILE cc_start: 0.8396 (pt) cc_final: 0.8153 (pt) REVERT: D 79 GLU cc_start: 0.7889 (tt0) cc_final: 0.7679 (tp30) REVERT: D 86 TYR cc_start: 0.8246 (m-10) cc_final: 0.7554 (m-10) REVERT: D 101 VAL cc_start: 0.8622 (t) cc_final: 0.8350 (p) REVERT: D 102 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7678 (ttm110) REVERT: D 114 VAL cc_start: 0.8646 (t) cc_final: 0.8302 (p) REVERT: E 52 ARG cc_start: 0.7361 (tpm170) cc_final: 0.7150 (tpm170) REVERT: E 56 LYS cc_start: 0.9052 (tttp) cc_final: 0.8021 (tttp) REVERT: E 65 LEU cc_start: 0.8387 (tp) cc_final: 0.8031 (mm) REVERT: E 76 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7343 (tp-100) REVERT: E 93 GLN cc_start: 0.7464 (tp-100) cc_final: 0.6932 (tp40) REVERT: E 121 LYS cc_start: 0.8485 (ptmm) cc_final: 0.8159 (ttpp) REVERT: E 122 LYS cc_start: 0.8733 (mmpt) cc_final: 0.7722 (mmmm) REVERT: E 125 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7084 (pttm) REVERT: F 63 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6992 (tp30) REVERT: F 88 TYR cc_start: 0.7254 (m-10) cc_final: 0.6782 (m-10) REVERT: F 95 ARG cc_start: 0.7745 (ptp-170) cc_final: 0.7281 (ptt-90) REVERT: G 48 LYS cc_start: 0.7816 (mmpt) cc_final: 0.7549 (mmmt) REVERT: G 81 THR cc_start: 0.8449 (m) cc_final: 0.8236 (p) REVERT: G 94 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6758 (mm-30) REVERT: H 74 GLU cc_start: 0.7655 (tp30) cc_final: 0.7278 (tp30) REVERT: H 89 LYS cc_start: 0.8338 (tppp) cc_final: 0.8079 (mmmt) REVERT: H 91 THR cc_start: 0.9016 (t) cc_final: 0.8815 (p) REVERT: H 118 THR cc_start: 0.8619 (t) cc_final: 0.8416 (p) REVERT: K 167 LEU cc_start: 0.8737 (mm) cc_final: 0.8403 (tp) REVERT: K 170 ILE cc_start: 0.8723 (mt) cc_final: 0.8490 (pt) REVERT: K 251 LEU cc_start: 0.8385 (mt) cc_final: 0.7978 (mm) REVERT: K 292 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7351 (mmmt) REVERT: K 310 GLN cc_start: 0.6922 (pp30) cc_final: 0.6461 (pp30) REVERT: K 356 THR cc_start: 0.8780 (m) cc_final: 0.8263 (m) REVERT: K 357 LEU cc_start: 0.8305 (mt) cc_final: 0.7981 (mt) REVERT: K 372 GLU cc_start: 0.8141 (tt0) cc_final: 0.7900 (tt0) REVERT: K 406 ASN cc_start: 0.7439 (p0) cc_final: 0.7178 (p0) REVERT: L 40 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7040 (tp30) REVERT: L 44 PHE cc_start: 0.7598 (m-10) cc_final: 0.7300 (m-10) REVERT: M 209 MET cc_start: 0.6099 (ttp) cc_final: 0.5736 (ttp) REVERT: M 234 LEU cc_start: 0.6977 (mt) cc_final: 0.6758 (mt) REVERT: N 7 LEU cc_start: 0.8327 (pp) cc_final: 0.7971 (pp) REVERT: N 8 GLU cc_start: 0.8375 (mp0) cc_final: 0.7844 (mp0) REVERT: N 26 GLU cc_start: 0.7689 (tt0) cc_final: 0.7410 (tt0) REVERT: N 89 LEU cc_start: 0.7326 (pp) cc_final: 0.6732 (mt) outliers start: 2 outliers final: 0 residues processed: 508 average time/residue: 0.4034 time to fit residues: 280.6580 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 : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.0030 chunk 66 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089871 restraints weight = 59117.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092158 restraints weight = 32508.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093630 restraints weight = 20964.547| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18310 Z= 0.172 Angle : 0.716 11.604 25948 Z= 0.394 Chirality : 0.041 0.219 2924 Planarity : 0.005 0.071 2268 Dihedral : 28.509 88.269 4818 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1373 helix: -0.45 (0.19), residues: 715 sheet: -1.48 (1.02), residues: 26 loop : -2.16 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 353 HIS 0.005 0.001 HIS H 52 PHE 0.032 0.002 PHE N 21 TYR 0.023 0.002 TYR F 98 ARG 0.012 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 821) hydrogen bonds : angle 4.09462 ( 2079) covalent geometry : bond 0.00382 (18310) covalent geometry : angle 0.71602 (25948) *********************** 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 512 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7416 (m-30) cc_final: 0.6997 (m-30) REVERT: A 125 LYS cc_start: 0.8690 (tppt) cc_final: 0.8265 (tppt) REVERT: B 53 GLU cc_start: 0.7756 (pp20) cc_final: 0.7526 (pp20) REVERT: C 52 TYR cc_start: 0.5838 (t80) cc_final: 0.5547 (t80) REVERT: D 57 ILE cc_start: 0.8435 (mm) cc_final: 0.8194 (tp) REVERT: D 71 ASP cc_start: 0.7465 (p0) cc_final: 0.6996 (p0) REVERT: D 73 PHE cc_start: 0.7961 (t80) cc_final: 0.7716 (t80) REVERT: D 79 GLU cc_start: 0.7872 (tt0) cc_final: 0.7632 (tp30) REVERT: D 86 TYR cc_start: 0.8291 (m-10) cc_final: 0.7470 (m-10) REVERT: D 101 VAL cc_start: 0.8660 (t) cc_final: 0.8399 (p) REVERT: D 102 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7850 (ttm110) REVERT: D 114 VAL cc_start: 0.8692 (t) cc_final: 0.8162 (p) REVERT: E 56 LYS cc_start: 0.9129 (tttp) cc_final: 0.8214 (tttp) REVERT: E 58 THR cc_start: 0.8969 (p) cc_final: 0.8768 (p) REVERT: E 122 LYS cc_start: 0.8844 (mmpt) cc_final: 0.8179 (mmmm) REVERT: F 27 GLN cc_start: 0.8279 (pm20) cc_final: 0.7863 (pm20) REVERT: F 63 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7043 (tp30) REVERT: F 88 TYR cc_start: 0.7258 (m-10) cc_final: 0.6745 (m-10) REVERT: F 95 ARG cc_start: 0.7896 (ptp-170) cc_final: 0.7391 (ptp90) REVERT: G 66 GLU cc_start: 0.7280 (tp30) cc_final: 0.7024 (tp30) REVERT: G 87 LEU cc_start: 0.7228 (tp) cc_final: 0.6549 (tp) REVERT: G 94 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6883 (mm-30) REVERT: H 74 GLU cc_start: 0.7589 (tp30) cc_final: 0.7259 (tp30) REVERT: H 89 LYS cc_start: 0.8346 (tppp) cc_final: 0.8040 (mmmt) REVERT: K 310 GLN cc_start: 0.7046 (pp30) cc_final: 0.6632 (pp30) REVERT: K 350 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7823 (ttp-110) REVERT: K 356 THR cc_start: 0.8859 (m) cc_final: 0.8370 (m) REVERT: K 357 LEU cc_start: 0.8313 (mt) cc_final: 0.8020 (mt) REVERT: K 360 LEU cc_start: 0.8830 (tp) cc_final: 0.8535 (tp) REVERT: K 364 HIS cc_start: 0.7064 (t70) cc_final: 0.6845 (t70) REVERT: K 368 ILE cc_start: 0.7964 (pt) cc_final: 0.7745 (pt) REVERT: K 372 GLU cc_start: 0.8029 (tt0) cc_final: 0.7670 (pt0) REVERT: K 394 LEU cc_start: 0.8676 (pt) cc_final: 0.8471 (pp) REVERT: K 406 ASN cc_start: 0.7476 (p0) cc_final: 0.7209 (p0) REVERT: L 40 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6910 (tp30) REVERT: L 44 PHE cc_start: 0.7565 (m-10) cc_final: 0.7183 (m-10) REVERT: M 209 MET cc_start: 0.6200 (ttp) cc_final: 0.5817 (ttp) REVERT: M 353 LYS cc_start: 0.9045 (mptt) cc_final: 0.8815 (mptt) REVERT: N 7 LEU cc_start: 0.8351 (pp) cc_final: 0.7974 (pp) REVERT: N 8 GLU cc_start: 0.8347 (mp0) cc_final: 0.7837 (mp0) REVERT: N 26 GLU cc_start: 0.7652 (tt0) cc_final: 0.7389 (tt0) REVERT: N 89 LEU cc_start: 0.7124 (pp) cc_final: 0.6526 (mt) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3889 time to fit residues: 271.7227 Evaluate side-chains 460 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS C 84 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS ** 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 = 0.3814 r_free = 0.3814 target = 0.106829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090165 restraints weight = 58753.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092552 restraints weight = 31702.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094080 restraints weight = 20318.132| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18310 Z= 0.172 Angle : 0.727 11.197 25948 Z= 0.400 Chirality : 0.041 0.219 2924 Planarity : 0.005 0.076 2268 Dihedral : 28.470 88.237 4818 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1373 helix: -0.38 (0.19), residues: 702 sheet: -1.54 (1.01), residues: 26 loop : -2.12 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 353 HIS 0.011 0.001 HIS C 38 PHE 0.035 0.002 PHE A 104 TYR 0.018 0.002 TYR B 72 ARG 0.012 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 821) hydrogen bonds : angle 4.17173 ( 2079) covalent geometry : bond 0.00387 (18310) covalent geometry : angle 0.72666 (25948) *********************** 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 512 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.819 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: 0.8709 (m-80) cc_final: 0.8349 (m-80) REVERT: A 59 GLU cc_start: 0.8060 (pm20) cc_final: 0.7741 (pm20) REVERT: A 125 LYS cc_start: 0.8698 (tppt) cc_final: 0.8253 (tppt) REVERT: B 39 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.8053 (mmm-85) REVERT: C 52 TYR cc_start: 0.5905 (t80) cc_final: 0.5638 (t80) REVERT: D 46 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8154 (mmpt) REVERT: D 57 ILE cc_start: 0.8487 (mm) cc_final: 0.8156 (tp) REVERT: D 71 ASP cc_start: 0.7440 (p0) cc_final: 0.7085 (p0) REVERT: D 73 PHE cc_start: 0.8007 (t80) cc_final: 0.7771 (t80) REVERT: D 76 ILE cc_start: 0.8415 (pt) cc_final: 0.7974 (pt) REVERT: D 86 TYR cc_start: 0.8322 (m-10) cc_final: 0.7544 (m-10) REVERT: D 101 VAL cc_start: 0.8696 (t) cc_final: 0.8486 (p) REVERT: D 102 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7606 (ttm110) REVERT: D 114 VAL cc_start: 0.8486 (t) cc_final: 0.7903 (t) REVERT: E 116 ARG cc_start: 0.7005 (mtm110) cc_final: 0.6802 (mtm110) REVERT: E 130 LEU cc_start: 0.8467 (tp) cc_final: 0.8198 (mt) REVERT: F 27 GLN cc_start: 0.7862 (pm20) cc_final: 0.7041 (pm20) REVERT: F 63 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7059 (tp30) REVERT: F 82 THR cc_start: 0.8745 (t) cc_final: 0.8440 (t) REVERT: F 88 TYR cc_start: 0.7349 (m-10) cc_final: 0.6825 (m-10) REVERT: F 95 ARG cc_start: 0.8039 (ptp-170) cc_final: 0.7473 (ptp90) REVERT: G 52 TYR cc_start: 0.7123 (t80) cc_final: 0.6774 (t80) REVERT: G 63 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7086 (mm-30) REVERT: G 66 GLU cc_start: 0.7346 (tp30) cc_final: 0.6977 (tm-30) REVERT: G 87 LEU cc_start: 0.7245 (tp) cc_final: 0.6068 (tp) REVERT: G 94 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7132 (mm-30) REVERT: H 74 GLU cc_start: 0.7660 (tp30) cc_final: 0.7383 (tp30) REVERT: K 170 ILE cc_start: 0.8659 (pt) cc_final: 0.8268 (mm) REVERT: K 245 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7632 (tmm160) REVERT: K 310 GLN cc_start: 0.7069 (pp30) cc_final: 0.6707 (pp30) REVERT: K 331 GLU cc_start: 0.7252 (pm20) cc_final: 0.6790 (pm20) REVERT: K 350 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7844 (ttp-110) REVERT: K 356 THR cc_start: 0.8921 (m) cc_final: 0.8422 (m) REVERT: K 357 LEU cc_start: 0.8435 (mt) cc_final: 0.8123 (mt) REVERT: K 372 GLU cc_start: 0.8098 (tt0) cc_final: 0.7887 (tt0) REVERT: K 407 GLU cc_start: 0.7906 (tp30) cc_final: 0.7697 (tp30) REVERT: M 209 MET cc_start: 0.6020 (ttp) cc_final: 0.5675 (ttp) REVERT: M 234 LEU cc_start: 0.7078 (mt) cc_final: 0.6871 (mt) REVERT: M 259 MET cc_start: 0.4497 (pmm) cc_final: 0.4283 (pmm) REVERT: M 353 LYS cc_start: 0.9077 (mptt) cc_final: 0.8822 (mptt) REVERT: N 7 LEU cc_start: 0.8255 (pp) cc_final: 0.7870 (pp) REVERT: N 8 GLU cc_start: 0.8361 (mp0) cc_final: 0.7867 (mp0) REVERT: N 26 GLU cc_start: 0.7635 (tt0) cc_final: 0.7331 (tt0) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3851 time to fit residues: 269.0718 Evaluate side-chains 466 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 98 GLN H 98 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS K 401 HIS ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN N 107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.108365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091911 restraints weight = 60089.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094109 restraints weight = 33819.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095512 restraints weight = 22465.009| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7542 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= 0.166 Angle : 0.738 11.592 25948 Z= 0.403 Chirality : 0.041 0.211 2924 Planarity : 0.005 0.076 2268 Dihedral : 28.436 87.948 4818 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.08 % Allowed : 1.12 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1373 helix: -0.33 (0.19), residues: 700 sheet: -1.37 (1.04), residues: 26 loop : -2.07 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 353 HIS 0.014 0.001 HIS F 75 PHE 0.020 0.002 PHE N 21 TYR 0.023 0.002 TYR F 98 ARG 0.011 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 821) hydrogen bonds : angle 4.10094 ( 2079) covalent geometry : bond 0.00371 (18310) covalent geometry : angle 0.73831 (25948) *********************** 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 503 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 2.666 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: A 53 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7981 (ttp80) REVERT: A 54 PHE cc_start: 0.8638 (m-80) cc_final: 0.8257 (m-80) REVERT: A 59 GLU cc_start: 0.7990 (pm20) cc_final: 0.7687 (pm20) REVERT: A 77 ASP cc_start: 0.8537 (p0) cc_final: 0.8223 (p0) REVERT: A 125 LYS cc_start: 0.8579 (tppt) cc_final: 0.8191 (tppt) REVERT: B 44 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8212 (ptpt) REVERT: C 52 TYR cc_start: 0.5931 (t80) cc_final: 0.5619 (t80) REVERT: D 46 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8169 (mmpt) REVERT: D 76 ILE cc_start: 0.8471 (pt) cc_final: 0.7878 (pt) REVERT: D 86 TYR cc_start: 0.8300 (m-10) cc_final: 0.7427 (m-10) REVERT: D 98 GLN cc_start: 0.7268 (tp-100) cc_final: 0.6850 (tm-30) REVERT: D 101 VAL cc_start: 0.8665 (t) cc_final: 0.8428 (p) REVERT: D 102 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7532 (ttm110) REVERT: D 114 VAL cc_start: 0.8470 (t) cc_final: 0.7823 (p) REVERT: D 118 THR cc_start: 0.7633 (m) cc_final: 0.7422 (m) REVERT: E 74 ILE cc_start: 0.8872 (mm) cc_final: 0.8024 (mm) REVERT: F 27 GLN cc_start: 0.7927 (pm20) cc_final: 0.6679 (pm20) REVERT: F 40 ARG cc_start: 0.8661 (tpp80) cc_final: 0.8335 (tpp80) REVERT: F 49 LEU cc_start: 0.8088 (tt) cc_final: 0.7678 (tp) REVERT: F 63 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7182 (mm-30) REVERT: F 88 TYR cc_start: 0.7153 (m-10) cc_final: 0.6831 (m-10) REVERT: F 95 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7521 (ptp90) REVERT: G 44 ARG cc_start: 0.6854 (tpt90) cc_final: 0.5966 (tpt90) REVERT: G 48 LYS cc_start: 0.7631 (mmpt) cc_final: 0.7429 (mmpt) REVERT: G 52 TYR cc_start: 0.6981 (t80) cc_final: 0.6681 (t80) REVERT: G 63 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6738 (mm-30) REVERT: G 66 GLU cc_start: 0.7327 (tp30) cc_final: 0.7058 (tm-30) REVERT: G 87 LEU cc_start: 0.7063 (tp) cc_final: 0.6106 (tp) REVERT: G 94 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6794 (mm-30) REVERT: H 74 GLU cc_start: 0.7459 (tp30) cc_final: 0.7239 (tp30) REVERT: H 87 ASN cc_start: 0.7840 (t0) cc_final: 0.7538 (t0) REVERT: H 108 GLU cc_start: 0.6865 (pm20) cc_final: 0.5232 (pm20) REVERT: H 119 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8205 (ttp-110) REVERT: K 170 ILE cc_start: 0.8532 (pt) cc_final: 0.8150 (mm) REVERT: K 350 ARG cc_start: 0.7993 (ptp90) cc_final: 0.7708 (ttp-110) REVERT: K 356 THR cc_start: 0.8928 (m) cc_final: 0.8466 (m) REVERT: K 357 LEU cc_start: 0.8435 (mt) cc_final: 0.8194 (mt) REVERT: K 407 GLU cc_start: 0.7906 (tp30) cc_final: 0.7693 (tp30) REVERT: M 209 MET cc_start: 0.6135 (ttp) cc_final: 0.5767 (ttp) REVERT: M 249 PHE cc_start: 0.6217 (t80) cc_final: 0.5555 (t80) REVERT: M 254 ASP cc_start: 0.8466 (p0) cc_final: 0.8266 (p0) REVERT: M 259 MET cc_start: 0.4456 (pmm) cc_final: 0.4255 (pmm) REVERT: M 353 LYS cc_start: 0.9038 (mptt) cc_final: 0.8777 (mptt) REVERT: N 7 LEU cc_start: 0.8161 (pp) cc_final: 0.7897 (pp) REVERT: N 8 GLU cc_start: 0.8351 (mp0) cc_final: 0.7912 (mp0) REVERT: N 26 GLU cc_start: 0.7570 (tt0) cc_final: 0.7310 (tt0) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.4004 time to fit residues: 276.4888 Evaluate side-chains 461 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 118 optimal weight: 0.0040 chunk 37 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS N 91 ASN N 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.108183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091764 restraints weight = 59706.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.093975 restraints weight = 33816.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095402 restraints weight = 22469.747| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18310 Z= 0.176 Angle : 0.743 11.008 25948 Z= 0.407 Chirality : 0.042 0.239 2924 Planarity : 0.005 0.078 2268 Dihedral : 28.402 87.998 4818 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.22), residues: 1373 helix: -0.39 (0.19), residues: 704 sheet: -1.41 (1.03), residues: 26 loop : -2.06 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 279 HIS 0.013 0.001 HIS F 75 PHE 0.026 0.002 PHE D 73 TYR 0.034 0.002 TYR M 278 ARG 0.013 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 821) hydrogen bonds : angle 4.18143 ( 2079) covalent geometry : bond 0.00397 (18310) covalent geometry : angle 0.74283 (25948) ********************** 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 504 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 2.221 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 49 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7052 (mmm160) REVERT: A 53 ARG cc_start: 0.8248 (ttp80) cc_final: 0.8015 (ttp80) REVERT: A 54 PHE cc_start: 0.8608 (m-80) cc_final: 0.8355 (m-80) REVERT: A 57 SER cc_start: 0.8153 (p) cc_final: 0.7713 (p) REVERT: A 77 ASP cc_start: 0.8557 (p0) cc_final: 0.8238 (p0) REVERT: A 106 ASP cc_start: 0.6984 (m-30) cc_final: 0.6300 (m-30) REVERT: A 125 LYS cc_start: 0.8577 (tppt) cc_final: 0.8193 (tppt) REVERT: A 128 ARG cc_start: 0.8914 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: A 131 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8272 (tpp80) REVERT: B 44 LYS cc_start: 0.8641 (ptpp) cc_final: 0.7915 (ptpt) REVERT: B 59 LYS cc_start: 0.8914 (tppp) cc_final: 0.8645 (tppp) REVERT: C 52 TYR cc_start: 0.5879 (t80) cc_final: 0.5653 (t80) REVERT: D 46 LYS cc_start: 0.8390 (mmpt) cc_final: 0.8089 (mmpt) REVERT: D 74 GLU cc_start: 0.7350 (tp30) cc_final: 0.6907 (tp30) REVERT: D 76 ILE cc_start: 0.8319 (pt) cc_final: 0.7915 (pt) REVERT: D 86 TYR cc_start: 0.8354 (m-10) cc_final: 0.7332 (m-10) REVERT: D 101 VAL cc_start: 0.8732 (t) cc_final: 0.8445 (p) REVERT: D 114 VAL cc_start: 0.8616 (t) cc_final: 0.8167 (p) REVERT: E 73 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6596 (mt-10) REVERT: E 74 ILE cc_start: 0.8856 (mm) cc_final: 0.8631 (mm) REVERT: E 116 ARG cc_start: 0.6878 (mtm110) cc_final: 0.6592 (ttm170) REVERT: E 122 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8422 (mmmm) REVERT: F 49 LEU cc_start: 0.8070 (tt) cc_final: 0.7717 (tp) REVERT: F 50 ILE cc_start: 0.8727 (tp) cc_final: 0.8447 (tp) REVERT: F 63 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6871 (tp30) REVERT: F 88 TYR cc_start: 0.7096 (m-10) cc_final: 0.6762 (m-10) REVERT: F 95 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7662 (ptp90) REVERT: G 63 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6876 (mm-30) REVERT: G 66 GLU cc_start: 0.7287 (tp30) cc_final: 0.7048 (tm-30) REVERT: G 87 LEU cc_start: 0.7185 (tp) cc_final: 0.6076 (tp) REVERT: G 94 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6780 (mm-30) REVERT: H 74 GLU cc_start: 0.7513 (tp30) cc_final: 0.7148 (tp30) REVERT: K 292 LYS cc_start: 0.7492 (mmpt) cc_final: 0.7288 (mmmt) REVERT: K 350 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7726 (ttp-110) REVERT: K 356 THR cc_start: 0.8879 (m) cc_final: 0.8426 (m) REVERT: K 357 LEU cc_start: 0.8509 (mt) cc_final: 0.8216 (mt) REVERT: K 368 ILE cc_start: 0.8245 (pt) cc_final: 0.7986 (pt) REVERT: K 407 GLU cc_start: 0.7998 (tp30) cc_final: 0.7710 (tp30) REVERT: L 40 GLU cc_start: 0.7661 (tp30) cc_final: 0.7378 (tp30) REVERT: M 209 MET cc_start: 0.6106 (ttp) cc_final: 0.5743 (ttp) REVERT: M 249 PHE cc_start: 0.6324 (t80) cc_final: 0.5680 (t80) REVERT: M 254 ASP cc_start: 0.8438 (p0) cc_final: 0.8216 (p0) REVERT: M 353 LYS cc_start: 0.9034 (mptt) cc_final: 0.8734 (mptt) REVERT: N 7 LEU cc_start: 0.8084 (pp) cc_final: 0.7829 (pp) REVERT: N 8 GLU cc_start: 0.8416 (mp0) cc_final: 0.7927 (mp0) REVERT: N 26 GLU cc_start: 0.7643 (tt0) cc_final: 0.7367 (tt0) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.4439 time to fit residues: 307.6363 Evaluate side-chains 460 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS D 98 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN K 222 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 356 ASN N 91 ASN N 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.105496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088718 restraints weight = 59409.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090895 restraints weight = 33738.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092321 restraints weight = 22527.997| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.8311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18310 Z= 0.230 Angle : 0.813 12.131 25948 Z= 0.447 Chirality : 0.045 0.223 2924 Planarity : 0.006 0.084 2268 Dihedral : 28.504 89.340 4818 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.08 % Allowed : 1.12 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1373 helix: -0.52 (0.19), residues: 716 sheet: -1.07 (1.10), residues: 26 loop : -2.22 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 353 HIS 0.013 0.002 HIS F 75 PHE 0.028 0.002 PHE H 68 TYR 0.034 0.002 TYR G 52 ARG 0.013 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 821) hydrogen bonds : angle 4.24923 ( 2079) covalent geometry : bond 0.00521 (18310) covalent geometry : angle 0.81342 (25948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7458.39 seconds wall clock time: 133 minutes 9.40 seconds (7989.40 seconds total)