Starting phenix.real_space_refine on Thu Mar 5 00:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2y_13784/03_2026/7q2y_13784.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 60 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11115 2.51 5 N 2975 2.21 5 O 3503 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3413 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3102 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2251 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 279} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7776 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 24, 'TRANS': 951} Chain breaks: 10 Chain: "F" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "G" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.84, per 1000 atoms: 0.22 Number of scatterers: 17754 At special positions: 0 Unit cell: (118.77, 145.52, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 91 16.00 P 60 15.00 Mg 2 11.99 F 6 9.00 O 3503 8.00 N 2975 7.00 C 11115 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 608.0 milliseconds 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 9 sheets defined 67.3% alpha, 8.2% beta 26 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 removed outlier: 3.587A pdb=" N LEU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 50 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.549A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 174 through 202 removed outlier: 3.675A pdb=" N LYS A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 228 removed outlier: 3.506A pdb=" N LYS A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'A' and resid 985 through 1048 removed outlier: 3.552A pdb=" N MET A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1104 Processing helix chain 'A' and resid 1119 through 1133 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.160A pdb=" N PHE A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 191 through 202 removed outlier: 4.357A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 350 removed outlier: 3.557A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1287 Processing helix chain 'B' and resid 1300 through 1305 removed outlier: 4.015A pdb=" N GLU B1304 " --> pdb=" O ASP B1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1343 Processing helix chain 'B' and resid 1358 through 1372 Processing helix chain 'B' and resid 1384 through 1390 removed outlier: 3.734A pdb=" N PHE B1388 " --> pdb=" O ARG B1384 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 71 through 105 Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.673A pdb=" N THR C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 198 removed outlier: 4.045A pdb=" N GLY C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.723A pdb=" N GLU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 668 Processing helix chain 'C' and resid 692 through 702 removed outlier: 3.553A pdb=" N LYS C 701 " --> pdb=" O GLN C 697 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET C 702 " --> pdb=" O GLY C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 removed outlier: 3.506A pdb=" N ASP C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 727 Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 66 through 92 removed outlier: 3.689A pdb=" N GLN D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 131 removed outlier: 4.909A pdb=" N GLU D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 176 Processing helix chain 'D' and resid 185 through 205 Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 212 through 230 Processing helix chain 'D' and resid 232 through 247 Processing helix chain 'D' and resid 250 through 266 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 288 through 305 Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.053A pdb=" N MET D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 324 through 343 Processing helix chain 'D' and resid 345 through 366 removed outlier: 7.052A pdb=" N GLN D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN D 355 " --> pdb=" O HIS D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 388 Processing helix chain 'D' and resid 392 through 407 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 440 through 455 Processing helix chain 'D' and resid 518 through 551 Processing helix chain 'D' and resid 555 through 572 Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.601A pdb=" N GLY D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 613 Processing helix chain 'D' and resid 620 through 638 removed outlier: 3.736A pdb=" N GLY D 638 " --> pdb=" O ASN D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 658 removed outlier: 3.611A pdb=" N GLN D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 674 Processing helix chain 'D' and resid 697 through 714 Processing helix chain 'D' and resid 715 through 720 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 731 through 737 Processing helix chain 'D' and resid 737 through 752 removed outlier: 3.980A pdb=" N CYS D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 781 Processing helix chain 'D' and resid 787 through 803 removed outlier: 3.501A pdb=" N MET D 791 " --> pdb=" O GLU D 787 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 793 " --> pdb=" O TYR D 789 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 794 " --> pdb=" O PRO D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 821 Processing helix chain 'D' and resid 838 through 874 Processing helix chain 'D' and resid 910 through 928 removed outlier: 5.094A pdb=" N LEU D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU D 926 " --> pdb=" O GLU D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 935 through 946 removed outlier: 4.212A pdb=" N ILE D 939 " --> pdb=" O LYS D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 951 Processing helix chain 'D' and resid 952 through 968 Processing helix chain 'D' and resid 970 through 988 Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 990 through 1007 Processing helix chain 'D' and resid 1008 through 1012 removed outlier: 3.662A pdb=" N LEU D1011 " --> pdb=" O PHE D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1022 removed outlier: 4.244A pdb=" N LEU D1019 " --> pdb=" O ASN D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1045 Processing helix chain 'D' and resid 1052 through 1057 Processing helix chain 'D' and resid 1058 through 1062 removed outlier: 3.928A pdb=" N ASP D1061 " --> pdb=" O LYS D1058 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D1062 " --> pdb=" O CYS D1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1058 through 1062' Processing helix chain 'D' and resid 1067 through 1078 removed outlier: 4.015A pdb=" N CYS D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1100 removed outlier: 4.645A pdb=" N ILE D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP D1091 " --> pdb=" O ASN D1087 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP D1100 " --> pdb=" O LEU D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1118 removed outlier: 3.681A pdb=" N PHE D1117 " --> pdb=" O PHE D1113 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D1118 " --> pdb=" O LEU D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1138 Processing helix chain 'D' and resid 1141 through 1154 Processing helix chain 'D' and resid 1158 through 1166 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.688A pdb=" N GLU A 5 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.490A pdb=" N TYR A1109 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A1142 " --> pdb=" O TYR A1109 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A1111 " --> pdb=" O VAL A1142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1051 through 1056 removed outlier: 4.775A pdb=" N VAL A1071 " --> pdb=" O LYS A1078 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 173 removed outlier: 7.235A pdb=" N SER B 152 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 241 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 7.235A pdb=" N SER B 152 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 241 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 270 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.809A pdb=" N GLN B1393 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id=AA8, first strand: chain 'C' and resid 209 through 210 removed outlier: 4.026A pdb=" N ASN C 209 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 690 through 691 removed outlier: 3.502A pdb=" N LEU C 690 " --> pdb=" O VAL C 742 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5063 1.34 - 1.45: 2699 1.45 - 1.57: 10090 1.57 - 1.69: 116 1.69 - 1.81: 153 Bond restraints: 18121 Sorted by residual: bond pdb=" F2 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" F2 BEF B2002 " pdb="BE BEF B2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" F3 BEF B2002 " pdb="BE BEF B2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" F3 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N LEU D 179 " pdb=" CA LEU D 179 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.99e+00 ... (remaining 18116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 24369 2.48 - 4.97: 230 4.97 - 7.45: 35 7.45 - 9.93: 3 9.93 - 12.41: 2 Bond angle restraints: 24639 Sorted by residual: angle pdb=" N GLU D 364 " pdb=" CA GLU D 364 " pdb=" CB GLU D 364 " ideal model delta sigma weight residual 110.16 116.53 -6.37 1.48e+00 4.57e-01 1.85e+01 angle pdb=" N GLU D 114 " pdb=" CA GLU D 114 " pdb=" CB GLU D 114 " ideal model delta sigma weight residual 110.12 116.21 -6.09 1.47e+00 4.63e-01 1.72e+01 angle pdb=" F2 BEF B2002 " pdb="BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 119.96 107.55 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" F2 BEF A2002 " pdb="BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 119.96 107.65 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C LYS D1058 " pdb=" N CYS D1059 " pdb=" CA CYS D1059 " ideal model delta sigma weight residual 122.56 115.88 6.68 1.72e+00 3.38e-01 1.51e+01 ... (remaining 24634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 10672 35.30 - 70.61: 350 70.61 - 105.91: 17 105.91 - 141.22: 3 141.22 - 176.52: 2 Dihedral angle restraints: 11044 sinusoidal: 4963 harmonic: 6081 Sorted by residual: dihedral pdb=" CD ARG A 215 " pdb=" NE ARG A 215 " pdb=" CZ ARG A 215 " pdb=" NH1 ARG A 215 " ideal model delta sinusoidal sigma weight residual 0.00 -75.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" O1B ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PB ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 75.18 -135.18 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual 300.00 175.18 124.83 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 11041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2218 0.042 - 0.085: 494 0.085 - 0.127: 145 0.127 - 0.170: 13 0.170 - 0.212: 3 Chirality restraints: 2873 Sorted by residual: chirality pdb=" CA GLU A 219 " pdb=" N GLU A 219 " pdb=" C GLU A 219 " pdb=" CB GLU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG A 215 " pdb=" N ARG A 215 " pdb=" C ARG A 215 " pdb=" CB ARG A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB THR D1076 " pdb=" CA THR D1076 " pdb=" OG1 THR D1076 " pdb=" CG2 THR D1076 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 2870 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 215 " -1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG A 215 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 215 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 215 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1072 " 0.472 9.50e-02 1.11e+02 2.12e-01 2.74e+01 pdb=" NE ARG D1072 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG D1072 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D1072 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D1072 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 697 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C LYS D 697 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS D 697 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D 698 " 0.016 2.00e-02 2.50e+03 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 15826 3.19 - 3.76: 28258 3.76 - 4.33: 37392 4.33 - 4.90: 61666 Nonbonded interactions: 143317 Sorted by model distance: nonbonded pdb=" F3 BEF B2002 " pdb="MG MG B2003 " model vdw 2.047 2.120 nonbonded pdb=" O2B ADP A2001 " pdb="MG MG A2003 " model vdw 2.049 2.170 nonbonded pdb=" OE1 GLN A 147 " pdb="MG MG A2003 " model vdw 2.084 2.170 nonbonded pdb=" OG SER A 39 " pdb="MG MG A2003 " model vdw 2.100 2.170 nonbonded pdb=" O1B ADP B2001 " pdb="MG MG B2003 " model vdw 2.122 2.170 ... (remaining 143312 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.003 0.083 18121 Z= 0.164 Angle : 0.613 12.413 24639 Z= 0.343 Chirality : 0.040 0.212 2873 Planarity : 0.010 0.474 2905 Dihedral : 16.399 176.524 7068 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 0.42 % Allowed : 0.85 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 2032 helix: 2.63 (0.15), residues: 1286 sheet: 1.51 (0.40), residues: 175 loop : -0.97 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 221 TYR 0.014 0.001 TYR B 326 PHE 0.022 0.001 PHE A1149 TRP 0.004 0.001 TRP D1144 HIS 0.002 0.000 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00295 (18121) covalent geometry : angle 0.61280 (24639) hydrogen bonds : bond 0.09641 ( 1138) hydrogen bonds : angle 4.00014 ( 3317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 521 time to evaluate : 0.609 Fit side-chains REVERT: A 17 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7890 (ttt180) REVERT: A 62 LEU cc_start: 0.8573 (mt) cc_final: 0.8373 (mt) REVERT: A 90 ASN cc_start: 0.6826 (t0) cc_final: 0.6574 (t0) REVERT: A 155 ASN cc_start: 0.7897 (m110) cc_final: 0.7637 (m-40) REVERT: A 212 ASN cc_start: 0.7450 (m-40) cc_final: 0.7243 (m-40) REVERT: A 1075 ASN cc_start: 0.7744 (m110) cc_final: 0.7536 (m-40) REVERT: B 170 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7756 (ttmm) REVERT: B 208 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7969 (mmmm) REVERT: B 215 SER cc_start: 0.7359 (t) cc_final: 0.7002 (p) REVERT: B 216 ASP cc_start: 0.6752 (m-30) cc_final: 0.6523 (m-30) REVERT: B 276 GLU cc_start: 0.7489 (tp30) cc_final: 0.7197 (mm-30) REVERT: B 1271 PHE cc_start: 0.7754 (t80) cc_final: 0.7371 (t80) REVERT: B 1281 MET cc_start: 0.8207 (tpp) cc_final: 0.7958 (tpp) REVERT: B 1292 GLU cc_start: 0.5937 (tt0) cc_final: 0.5664 (tt0) REVERT: B 1358 ASP cc_start: 0.6313 (t70) cc_final: 0.6041 (t70) REVERT: C 56 TYR cc_start: 0.8020 (m-10) cc_final: 0.7758 (m-10) REVERT: C 73 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: C 213 THR cc_start: 0.7873 (p) cc_final: 0.7603 (p) REVERT: C 664 GLU cc_start: 0.7276 (tp30) cc_final: 0.6397 (tp30) REVERT: D 62 PHE cc_start: 0.5735 (m-10) cc_final: 0.5476 (m-10) REVERT: D 120 GLN cc_start: 0.8233 (tm130) cc_final: 0.7829 (tm-30) REVERT: D 163 GLN cc_start: 0.7949 (pt0) cc_final: 0.7415 (pm20) REVERT: D 166 ASN cc_start: 0.7658 (m110) cc_final: 0.7113 (m110) REVERT: D 203 LEU cc_start: 0.7754 (tp) cc_final: 0.7484 (tm) REVERT: D 259 LYS cc_start: 0.7998 (tttm) cc_final: 0.7553 (tttp) REVERT: D 263 ASP cc_start: 0.6258 (m-30) cc_final: 0.5761 (m-30) REVERT: D 264 GLU cc_start: 0.6234 (mp0) cc_final: 0.5743 (mp0) REVERT: D 303 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6504 (tm-30) REVERT: D 364 GLU cc_start: 0.6781 (mp0) cc_final: 0.6267 (mp0) REVERT: D 398 LYS cc_start: 0.7796 (tptm) cc_final: 0.7588 (tppp) REVERT: D 424 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7422 (ttmm) REVERT: D 573 ASP cc_start: 0.6367 (m-30) cc_final: 0.6133 (m-30) REVERT: D 655 TYR cc_start: 0.8274 (t80) cc_final: 0.8037 (t80) REVERT: D 714 ASP cc_start: 0.6194 (m-30) cc_final: 0.5897 (m-30) REVERT: D 872 LYS cc_start: 0.7893 (tttm) cc_final: 0.7548 (tppp) REVERT: D 972 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7785 (mtpp) REVERT: D 1070 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7631 (mmt) REVERT: D 1075 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6689 (m-80) outliers start: 8 outliers final: 2 residues processed: 524 average time/residue: 0.6224 time to fit residues: 361.3132 Evaluate side-chains 474 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 469 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 100 GLN A 193 GLN B 171 GLN B 193 ASN B 266 ASN B1319 ASN B1361 ASN B1385 ASN D 111 HIS D 120 GLN D 127 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 ASN D1010 ASN D1065 GLN D1128 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133124 restraints weight = 24070.285| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.82 r_work: 0.3458 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18121 Z= 0.133 Angle : 0.563 7.576 24639 Z= 0.296 Chirality : 0.040 0.195 2873 Planarity : 0.004 0.043 2905 Dihedral : 16.972 176.242 2884 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 2.65 % Allowed : 13.75 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.19), residues: 2032 helix: 2.70 (0.14), residues: 1288 sheet: 1.68 (0.41), residues: 175 loop : -0.86 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.021 0.001 TYR D 776 PHE 0.023 0.002 PHE B1388 TRP 0.005 0.001 TRP D 108 HIS 0.007 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00286 (18121) covalent geometry : angle 0.56254 (24639) hydrogen bonds : bond 0.04037 ( 1138) hydrogen bonds : angle 3.64137 ( 3317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 477 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 18 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 90 ASN cc_start: 0.7302 (t0) cc_final: 0.6990 (t0) REVERT: A 121 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7936 (ttt-90) REVERT: A 213 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 216 MET cc_start: 0.7474 (mmm) cc_final: 0.7143 (mmm) REVERT: A 1027 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 1038 LEU cc_start: 0.8472 (tp) cc_final: 0.8234 (tt) REVERT: A 1067 LEU cc_start: 0.8349 (mp) cc_final: 0.8043 (mt) REVERT: A 1159 ARG cc_start: 0.7588 (ttm110) cc_final: 0.7280 (ttm170) REVERT: A 1160 PHE cc_start: 0.8359 (t80) cc_final: 0.8065 (t80) REVERT: B 170 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8341 (ttmm) REVERT: B 208 LYS cc_start: 0.8223 (mmmm) cc_final: 0.8005 (mmmm) REVERT: B 216 ASP cc_start: 0.7666 (m-30) cc_final: 0.7426 (m-30) REVERT: B 1264 PHE cc_start: 0.7572 (t80) cc_final: 0.7357 (t80) REVERT: B 1271 PHE cc_start: 0.7943 (t80) cc_final: 0.7532 (t80) REVERT: B 1281 MET cc_start: 0.8632 (tpp) cc_final: 0.8340 (tpp) REVERT: B 1358 ASP cc_start: 0.7262 (t70) cc_final: 0.6958 (t70) REVERT: C 63 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6873 (pp) REVERT: C 73 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: C 285 MET cc_start: 0.7813 (mmm) cc_final: 0.7536 (mmm) REVERT: C 664 GLU cc_start: 0.7717 (tp30) cc_final: 0.7497 (tp30) REVERT: D 62 PHE cc_start: 0.5821 (m-10) cc_final: 0.5601 (m-10) REVERT: D 120 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 163 GLN cc_start: 0.8223 (pt0) cc_final: 0.7672 (pm20) REVERT: D 166 ASN cc_start: 0.7916 (m110) cc_final: 0.7444 (m110) REVERT: D 259 LYS cc_start: 0.8337 (tttm) cc_final: 0.7909 (tttp) REVERT: D 263 ASP cc_start: 0.7550 (m-30) cc_final: 0.7087 (m-30) REVERT: D 264 GLU cc_start: 0.7206 (mp0) cc_final: 0.6706 (mp0) REVERT: D 303 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7188 (tm-30) REVERT: D 364 GLU cc_start: 0.7442 (mp0) cc_final: 0.6922 (mp0) REVERT: D 365 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 398 LYS cc_start: 0.8132 (tptm) cc_final: 0.7812 (tptm) REVERT: D 402 LEU cc_start: 0.7848 (mt) cc_final: 0.7634 (mm) REVERT: D 424 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8026 (ttmm) REVERT: D 554 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7722 (mtpp) REVERT: D 573 ASP cc_start: 0.6968 (m-30) cc_final: 0.6724 (m-30) REVERT: D 578 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 579 PHE cc_start: 0.7809 (t80) cc_final: 0.7572 (t80) REVERT: D 602 VAL cc_start: 0.7428 (m) cc_final: 0.7130 (p) REVERT: D 787 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 944 VAL cc_start: 0.8511 (m) cc_final: 0.8310 (t) REVERT: D 972 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8235 (mtpp) REVERT: D 1025 ASP cc_start: 0.7959 (t70) cc_final: 0.7417 (m-30) REVERT: D 1075 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7088 (m-80) outliers start: 50 outliers final: 11 residues processed: 490 average time/residue: 0.6109 time to fit residues: 332.5215 Evaluate side-chains 484 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 469 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 195 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 100 GLN A 155 ASN A 193 GLN B 171 GLN B1385 ASN D 111 HIS D 127 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS D 765 GLN D1010 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133718 restraints weight = 24523.668| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.80 r_work: 0.3462 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18121 Z= 0.111 Angle : 0.530 6.927 24639 Z= 0.277 Chirality : 0.038 0.227 2873 Planarity : 0.003 0.050 2905 Dihedral : 17.000 178.522 2878 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 2.87 % Allowed : 16.40 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.19), residues: 2032 helix: 2.77 (0.14), residues: 1287 sheet: 1.71 (0.41), residues: 175 loop : -0.85 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1360 TYR 0.020 0.001 TYR D 776 PHE 0.025 0.001 PHE C 170 TRP 0.004 0.001 TRP D 108 HIS 0.007 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00233 (18121) covalent geometry : angle 0.52990 (24639) hydrogen bonds : bond 0.03643 ( 1138) hydrogen bonds : angle 3.58847 ( 3317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 476 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8409 (p) cc_final: 0.8200 (t) REVERT: A 53 SER cc_start: 0.8241 (t) cc_final: 0.7724 (p) REVERT: A 90 ASN cc_start: 0.7297 (t0) cc_final: 0.6976 (t0) REVERT: A 121 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7956 (ttt-90) REVERT: A 210 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 216 MET cc_start: 0.7289 (mmm) cc_final: 0.6836 (mmm) REVERT: A 1027 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7426 (tm-30) REVERT: A 1038 LEU cc_start: 0.8364 (tp) cc_final: 0.8139 (tt) REVERT: A 1067 LEU cc_start: 0.8328 (mp) cc_final: 0.8028 (mt) REVERT: A 1159 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7212 (ttm170) REVERT: B 170 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8325 (ttmm) REVERT: B 208 LYS cc_start: 0.8224 (mmmm) cc_final: 0.7991 (mmmm) REVERT: B 1254 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.4949 (mp0) REVERT: B 1264 PHE cc_start: 0.7609 (t80) cc_final: 0.7373 (t80) REVERT: B 1271 PHE cc_start: 0.7913 (t80) cc_final: 0.7542 (t80) REVERT: B 1281 MET cc_start: 0.8606 (tpp) cc_final: 0.8327 (tpp) REVERT: B 1358 ASP cc_start: 0.7180 (t70) cc_final: 0.6872 (t70) REVERT: C 30 ASN cc_start: 0.7541 (m110) cc_final: 0.7137 (m110) REVERT: C 39 THR cc_start: 0.7902 (m) cc_final: 0.7655 (m) REVERT: C 63 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6793 (pp) REVERT: C 211 ASP cc_start: 0.7436 (t0) cc_final: 0.7134 (t0) REVERT: C 664 GLU cc_start: 0.7707 (tp30) cc_final: 0.7498 (tp30) REVERT: D 120 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7779 (tm130) REVERT: D 163 GLN cc_start: 0.8213 (pt0) cc_final: 0.7742 (pt0) REVERT: D 166 ASN cc_start: 0.7877 (m110) cc_final: 0.7433 (m110) REVERT: D 193 ILE cc_start: 0.7690 (mm) cc_final: 0.7338 (mm) REVERT: D 264 GLU cc_start: 0.7181 (mp0) cc_final: 0.6780 (mp0) REVERT: D 324 SER cc_start: 0.8208 (t) cc_final: 0.7809 (m) REVERT: D 331 VAL cc_start: 0.8392 (t) cc_final: 0.8124 (t) REVERT: D 364 GLU cc_start: 0.7594 (mp0) cc_final: 0.7178 (mp0) REVERT: D 365 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 554 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7756 (mtpp) REVERT: D 578 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7260 (mm-30) REVERT: D 579 PHE cc_start: 0.7765 (t80) cc_final: 0.7543 (t80) REVERT: D 787 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 972 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8251 (mtpp) REVERT: D 1070 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: D 1075 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: D 1077 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6445 (mp0) outliers start: 54 outliers final: 18 residues processed: 491 average time/residue: 0.6091 time to fit residues: 332.5123 Evaluate side-chains 485 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 461 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 193 GLN A1075 ASN B 171 GLN B1385 ASN C 321 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126229 restraints weight = 23793.725| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.76 r_work: 0.3346 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18121 Z= 0.152 Angle : 0.573 7.542 24639 Z= 0.300 Chirality : 0.040 0.238 2873 Planarity : 0.003 0.043 2905 Dihedral : 17.051 177.377 2873 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 3.87 % Allowed : 17.20 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.19), residues: 2032 helix: 2.69 (0.14), residues: 1281 sheet: 1.73 (0.42), residues: 169 loop : -0.85 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 221 TYR 0.021 0.002 TYR D 776 PHE 0.025 0.002 PHE C 170 TRP 0.007 0.001 TRP C 49 HIS 0.007 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00344 (18121) covalent geometry : angle 0.57306 (24639) hydrogen bonds : bond 0.04419 ( 1138) hydrogen bonds : angle 3.75715 ( 3317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 498 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7706 (pt0) cc_final: 0.7410 (pt0) REVERT: A 18 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8175 (t) REVERT: A 20 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 53 SER cc_start: 0.8600 (t) cc_final: 0.8001 (p) REVERT: A 90 ASN cc_start: 0.7337 (t0) cc_final: 0.6991 (t0) REVERT: A 100 GLN cc_start: 0.7361 (tp-100) cc_final: 0.6665 (tp40) REVERT: A 216 MET cc_start: 0.7303 (mmm) cc_final: 0.6884 (mmm) REVERT: A 989 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.7027 (ttp) REVERT: A 1009 LYS cc_start: 0.8154 (mttt) cc_final: 0.7791 (mtmm) REVERT: A 1027 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 1067 LEU cc_start: 0.8403 (mp) cc_final: 0.8067 (mt) REVERT: A 1108 MET cc_start: 0.8293 (ptp) cc_final: 0.8076 (ptp) REVERT: A 1148 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7686 (mtm) REVERT: B 138 GLN cc_start: 0.7476 (mm110) cc_final: 0.7131 (mm110) REVERT: B 170 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8327 (ttmm) REVERT: B 274 GLU cc_start: 0.7694 (mp0) cc_final: 0.7491 (mp0) REVERT: B 1254 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4866 (mp0) REVERT: B 1264 PHE cc_start: 0.7768 (t80) cc_final: 0.7483 (t80) REVERT: B 1271 PHE cc_start: 0.8038 (t80) cc_final: 0.7718 (t80) REVERT: B 1281 MET cc_start: 0.8634 (tpp) cc_final: 0.8381 (tpp) REVERT: B 1358 ASP cc_start: 0.7264 (t70) cc_final: 0.7009 (t70) REVERT: C 30 ASN cc_start: 0.7719 (m-40) cc_final: 0.7407 (m-40) REVERT: C 73 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: C 101 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 211 ASP cc_start: 0.7788 (t0) cc_final: 0.7504 (t0) REVERT: C 285 MET cc_start: 0.7892 (mmm) cc_final: 0.7593 (mmm) REVERT: C 296 CYS cc_start: 0.7248 (p) cc_final: 0.6931 (p) REVERT: C 637 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 664 GLU cc_start: 0.7803 (tp30) cc_final: 0.7583 (tp30) REVERT: D 120 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7742 (tm130) REVERT: D 163 GLN cc_start: 0.8154 (pt0) cc_final: 0.7559 (pt0) REVERT: D 166 ASN cc_start: 0.7952 (m110) cc_final: 0.7520 (m110) REVERT: D 213 SER cc_start: 0.7495 (p) cc_final: 0.7242 (m) REVERT: D 264 GLU cc_start: 0.7340 (mp0) cc_final: 0.7010 (mp0) REVERT: D 281 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6912 (ttm-80) REVERT: D 317 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8561 (OUTLIER) REVERT: D 321 ASN cc_start: 0.8311 (m-40) cc_final: 0.8095 (m-40) REVERT: D 331 VAL cc_start: 0.8352 (t) cc_final: 0.8023 (p) REVERT: D 364 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7243 (mt-10) REVERT: D 365 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6988 (tm-30) REVERT: D 548 SER cc_start: 0.7964 (m) cc_final: 0.7676 (t) REVERT: D 573 ASP cc_start: 0.7223 (m-30) cc_final: 0.6932 (m-30) REVERT: D 578 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 579 PHE cc_start: 0.7832 (t80) cc_final: 0.7628 (t80) REVERT: D 590 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: D 610 GLN cc_start: 0.7607 (mm110) cc_final: 0.7355 (mm110) REVERT: D 787 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7465 (mm-30) REVERT: D 791 MET cc_start: 0.8762 (tmm) cc_final: 0.8544 (ttp) REVERT: D 918 GLN cc_start: 0.7126 (tp-100) cc_final: 0.6750 (tp-100) REVERT: D 972 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8397 (mtpp) REVERT: D 982 ILE cc_start: 0.8365 (mm) cc_final: 0.8064 (mp) REVERT: D 1075 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: D 1077 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: D 1130 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7519 (mtpp) outliers start: 73 outliers final: 26 residues processed: 526 average time/residue: 0.6465 time to fit residues: 376.2268 Evaluate side-chains 513 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 475 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 125 GLN A 193 GLN B 171 GLN B1272 ASN B1290 ASN B1385 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1087 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123289 restraints weight = 23780.837| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.79 r_work: 0.3305 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18121 Z= 0.181 Angle : 0.603 8.450 24639 Z= 0.313 Chirality : 0.041 0.190 2873 Planarity : 0.004 0.057 2905 Dihedral : 17.047 175.139 2873 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 4.19 % Allowed : 19.21 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 2032 helix: 2.54 (0.14), residues: 1286 sheet: 1.54 (0.42), residues: 170 loop : -0.89 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1400 TYR 0.023 0.002 TYR B 326 PHE 0.023 0.002 PHE A1149 TRP 0.016 0.001 TRP C 49 HIS 0.010 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00422 (18121) covalent geometry : angle 0.60306 (24639) hydrogen bonds : bond 0.04652 ( 1138) hydrogen bonds : angle 3.85520 ( 3317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 484 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7747 (pt0) cc_final: 0.7499 (pt0) REVERT: A 18 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8122 (t) REVERT: A 20 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7729 (mt) REVERT: A 53 SER cc_start: 0.8712 (t) cc_final: 0.8130 (p) REVERT: A 90 ASN cc_start: 0.7331 (t0) cc_final: 0.6982 (t0) REVERT: A 100 GLN cc_start: 0.7477 (tp-100) cc_final: 0.6904 (tp40) REVERT: A 114 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8068 (mmmm) REVERT: A 187 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8188 (ttmm) REVERT: A 216 MET cc_start: 0.7394 (mmm) cc_final: 0.6922 (mmm) REVERT: A 1009 LYS cc_start: 0.8214 (mttt) cc_final: 0.7872 (mtmm) REVERT: A 1015 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7778 (mt0) REVERT: A 1027 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 1042 ASN cc_start: 0.8573 (m-40) cc_final: 0.8343 (m-40) REVERT: A 1067 LEU cc_start: 0.8411 (mp) cc_final: 0.8075 (mt) REVERT: A 1148 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7763 (mtm) REVERT: B 138 GLN cc_start: 0.7451 (mm110) cc_final: 0.7123 (mm110) REVERT: B 170 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8332 (ttmm) REVERT: B 274 GLU cc_start: 0.7708 (mp0) cc_final: 0.7462 (mp0) REVERT: B 1254 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5013 (mp0) REVERT: B 1264 PHE cc_start: 0.7836 (t80) cc_final: 0.7534 (t80) REVERT: B 1271 PHE cc_start: 0.8098 (t80) cc_final: 0.7720 (t80) REVERT: B 1281 MET cc_start: 0.8775 (tpp) cc_final: 0.8517 (tpp) REVERT: B 1358 ASP cc_start: 0.7249 (t70) cc_final: 0.7030 (t70) REVERT: B 1360 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7866 (mtp180) REVERT: C 30 ASN cc_start: 0.7798 (m-40) cc_final: 0.7510 (m-40) REVERT: C 73 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (mp-120) REVERT: C 211 ASP cc_start: 0.7837 (t0) cc_final: 0.7576 (t0) REVERT: C 285 MET cc_start: 0.7867 (mmm) cc_final: 0.7586 (mmm) REVERT: C 637 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8037 (m) REVERT: C 664 GLU cc_start: 0.7789 (tp30) cc_final: 0.7519 (tp30) REVERT: D 120 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7756 (tm130) REVERT: D 163 GLN cc_start: 0.8156 (pt0) cc_final: 0.7789 (pt0) REVERT: D 166 ASN cc_start: 0.8074 (m110) cc_final: 0.7661 (m110) REVERT: D 213 SER cc_start: 0.7887 (p) cc_final: 0.7666 (m) REVERT: D 264 GLU cc_start: 0.7467 (mp0) cc_final: 0.7114 (mp0) REVERT: D 277 GLU cc_start: 0.8261 (tt0) cc_final: 0.7980 (tp30) REVERT: D 281 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7025 (ttm-80) REVERT: D 331 VAL cc_start: 0.8394 (t) cc_final: 0.8086 (p) REVERT: D 364 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 365 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6962 (tm-30) REVERT: D 380 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: D 548 SER cc_start: 0.8077 (m) cc_final: 0.7802 (t) REVERT: D 573 ASP cc_start: 0.7282 (m-30) cc_final: 0.7002 (m-30) REVERT: D 578 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7317 (mm-30) REVERT: D 610 GLN cc_start: 0.7860 (mm110) cc_final: 0.7580 (mm110) REVERT: D 657 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: D 787 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 791 MET cc_start: 0.8853 (tmm) cc_final: 0.8614 (ttp) REVERT: D 918 GLN cc_start: 0.7321 (tp-100) cc_final: 0.7002 (tp-100) REVERT: D 923 ASN cc_start: 0.7772 (m110) cc_final: 0.7563 (m-40) REVERT: D 972 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8411 (mtpp) REVERT: D 1075 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: D 1077 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: D 1130 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7466 (mtpp) outliers start: 79 outliers final: 34 residues processed: 522 average time/residue: 0.6301 time to fit residues: 364.1740 Evaluate side-chains 509 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 464 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 1022 ARG Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 193 GLN A1075 ASN B 132 ASN B 171 GLN B1272 ASN B1385 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 946 ASN D1027 ASN ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122441 restraints weight = 23565.263| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.78 r_work: 0.3286 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18121 Z= 0.176 Angle : 0.608 11.922 24639 Z= 0.314 Chirality : 0.041 0.173 2873 Planarity : 0.004 0.045 2905 Dihedral : 17.043 174.986 2873 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 4.67 % Allowed : 19.69 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 2032 helix: 2.48 (0.14), residues: 1288 sheet: 1.51 (0.41), residues: 169 loop : -0.93 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.024 0.002 TYR B 326 PHE 0.024 0.002 PHE A1149 TRP 0.018 0.001 TRP C 49 HIS 0.009 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00409 (18121) covalent geometry : angle 0.60821 (24639) hydrogen bonds : bond 0.04669 ( 1138) hydrogen bonds : angle 3.88138 ( 3317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 488 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7771 (pt0) cc_final: 0.7481 (pt0) REVERT: A 20 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 53 SER cc_start: 0.8680 (t) cc_final: 0.8203 (p) REVERT: A 90 ASN cc_start: 0.7347 (t0) cc_final: 0.6998 (t0) REVERT: A 100 GLN cc_start: 0.7504 (tp-100) cc_final: 0.6710 (tp40) REVERT: A 114 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8337 (mmmm) REVERT: A 132 GLN cc_start: 0.8707 (mt0) cc_final: 0.8474 (mt0) REVERT: A 187 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8117 (ttmm) REVERT: A 216 MET cc_start: 0.7421 (mmm) cc_final: 0.6944 (mmm) REVERT: A 1009 LYS cc_start: 0.8196 (mttt) cc_final: 0.7878 (mtmm) REVERT: A 1027 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 1042 ASN cc_start: 0.8649 (m-40) cc_final: 0.8442 (m-40) REVERT: A 1067 LEU cc_start: 0.8427 (mp) cc_final: 0.8079 (mt) REVERT: A 1108 MET cc_start: 0.8411 (ptp) cc_final: 0.8184 (ptp) REVERT: A 1157 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7316 (ttt-90) REVERT: B 138 GLN cc_start: 0.7488 (mm110) cc_final: 0.7160 (mm110) REVERT: B 170 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8359 (ttmm) REVERT: B 274 GLU cc_start: 0.7683 (mp0) cc_final: 0.7436 (mp0) REVERT: B 335 ASN cc_start: 0.7513 (m-40) cc_final: 0.7267 (m-40) REVERT: B 1254 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5014 (mp0) REVERT: B 1264 PHE cc_start: 0.7829 (t80) cc_final: 0.7539 (t80) REVERT: B 1281 MET cc_start: 0.8807 (tpp) cc_final: 0.8513 (tpp) REVERT: B 1360 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7855 (mtp180) REVERT: C 30 ASN cc_start: 0.7854 (m-40) cc_final: 0.7573 (m-40) REVERT: C 50 ASN cc_start: 0.7795 (m110) cc_final: 0.7524 (m110) REVERT: C 73 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7812 (mp-120) REVERT: C 87 SER cc_start: 0.8299 (m) cc_final: 0.8072 (p) REVERT: C 101 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 171 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 211 ASP cc_start: 0.7897 (t0) cc_final: 0.7644 (t0) REVERT: C 285 MET cc_start: 0.7883 (mmm) cc_final: 0.7586 (mmm) REVERT: C 637 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8050 (m) REVERT: C 664 GLU cc_start: 0.7773 (tp30) cc_final: 0.7506 (tp30) REVERT: D 120 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7685 (tm130) REVERT: D 163 GLN cc_start: 0.8173 (pt0) cc_final: 0.7814 (pt0) REVERT: D 166 ASN cc_start: 0.8068 (m110) cc_final: 0.7676 (m110) REVERT: D 213 SER cc_start: 0.8019 (p) cc_final: 0.7806 (m) REVERT: D 221 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7834 (ttm-80) REVERT: D 225 MET cc_start: 0.8504 (mtm) cc_final: 0.7737 (mtm) REVERT: D 264 GLU cc_start: 0.7514 (mp0) cc_final: 0.7250 (mp0) REVERT: D 277 GLU cc_start: 0.8265 (tt0) cc_final: 0.7982 (tp30) REVERT: D 281 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6988 (ttm-80) REVERT: D 331 VAL cc_start: 0.8372 (t) cc_final: 0.8069 (p) REVERT: D 364 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7436 (mt-10) REVERT: D 365 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6962 (tm-30) REVERT: D 380 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: D 573 ASP cc_start: 0.7316 (m-30) cc_final: 0.7096 (m-30) REVERT: D 578 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7344 (mm-30) REVERT: D 602 VAL cc_start: 0.8122 (m) cc_final: 0.7864 (p) REVERT: D 610 GLN cc_start: 0.7847 (mm110) cc_final: 0.7579 (mm110) REVERT: D 637 ILE cc_start: 0.8309 (pt) cc_final: 0.8061 (mt) REVERT: D 657 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: D 787 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 791 MET cc_start: 0.8816 (tmm) cc_final: 0.8597 (ttp) REVERT: D 918 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7118 (tp-100) REVERT: D 972 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8419 (mtpp) REVERT: D 982 ILE cc_start: 0.8428 (mm) cc_final: 0.8119 (mp) REVERT: D 1049 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7319 (p) REVERT: D 1075 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: D 1077 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: D 1130 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7497 (mtpp) outliers start: 88 outliers final: 44 residues processed: 528 average time/residue: 0.6417 time to fit residues: 374.5584 Evaluate side-chains 527 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 472 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1407 THR Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 1022 ARG Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 144 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 193 GLN B 171 GLN B1272 ASN B1290 ASN B1385 ASN D 111 HIS D 229 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122609 restraints weight = 23732.131| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.78 r_work: 0.3297 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18121 Z= 0.153 Angle : 0.602 11.344 24639 Z= 0.309 Chirality : 0.040 0.198 2873 Planarity : 0.004 0.057 2905 Dihedral : 17.033 174.839 2873 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 4.03 % Allowed : 21.66 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 2032 helix: 2.53 (0.14), residues: 1288 sheet: 1.49 (0.41), residues: 170 loop : -0.97 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1400 TYR 0.022 0.001 TYR B 326 PHE 0.022 0.002 PHE B1388 TRP 0.015 0.001 TRP C 49 HIS 0.012 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00352 (18121) covalent geometry : angle 0.60207 (24639) hydrogen bonds : bond 0.04479 ( 1138) hydrogen bonds : angle 3.87331 ( 3317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 478 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7792 (pt0) cc_final: 0.7591 (pt0) REVERT: A 20 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 53 SER cc_start: 0.8665 (t) cc_final: 0.8190 (p) REVERT: A 90 ASN cc_start: 0.7306 (t0) cc_final: 0.6946 (t0) REVERT: A 100 GLN cc_start: 0.7466 (tp-100) cc_final: 0.6705 (tp40) REVERT: A 108 VAL cc_start: 0.8070 (t) cc_final: 0.7799 (p) REVERT: A 114 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8301 (mmmm) REVERT: A 132 GLN cc_start: 0.8674 (mt0) cc_final: 0.8433 (mt0) REVERT: A 216 MET cc_start: 0.7376 (mmm) cc_final: 0.6903 (mmm) REVERT: A 989 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7283 (ttm) REVERT: A 1009 LYS cc_start: 0.8221 (mttt) cc_final: 0.7888 (mtmm) REVERT: A 1027 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 1042 ASN cc_start: 0.8603 (m-40) cc_final: 0.8381 (m-40) REVERT: A 1067 LEU cc_start: 0.8412 (mp) cc_final: 0.8052 (mt) REVERT: A 1108 MET cc_start: 0.8457 (ptp) cc_final: 0.8212 (ptp) REVERT: B 138 GLN cc_start: 0.7498 (mm110) cc_final: 0.7182 (mm110) REVERT: B 274 GLU cc_start: 0.7655 (mp0) cc_final: 0.7415 (mp0) REVERT: B 292 ASP cc_start: 0.7659 (t70) cc_final: 0.7156 (t70) REVERT: B 325 GLU cc_start: 0.7690 (mp0) cc_final: 0.7168 (mp0) REVERT: B 335 ASN cc_start: 0.7501 (m-40) cc_final: 0.7258 (m-40) REVERT: B 1254 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.4992 (mp0) REVERT: B 1264 PHE cc_start: 0.7792 (t80) cc_final: 0.7467 (t80) REVERT: B 1281 MET cc_start: 0.8779 (tpp) cc_final: 0.8476 (tpp) REVERT: C 30 ASN cc_start: 0.7856 (m-40) cc_final: 0.7579 (m-40) REVERT: C 50 ASN cc_start: 0.7794 (m110) cc_final: 0.7563 (m110) REVERT: C 80 ASP cc_start: 0.7488 (m-30) cc_final: 0.7242 (m-30) REVERT: C 87 SER cc_start: 0.8306 (m) cc_final: 0.8073 (p) REVERT: C 101 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8416 (mp) REVERT: C 171 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 211 ASP cc_start: 0.7865 (t0) cc_final: 0.7633 (t0) REVERT: C 637 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8039 (m) REVERT: C 664 GLU cc_start: 0.7748 (tp30) cc_final: 0.7489 (tp30) REVERT: C 708 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (mm) REVERT: D 120 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7755 (tm130) REVERT: D 163 GLN cc_start: 0.8172 (pt0) cc_final: 0.7811 (pt0) REVERT: D 166 ASN cc_start: 0.8064 (m110) cc_final: 0.7673 (m110) REVERT: D 213 SER cc_start: 0.8028 (p) cc_final: 0.7795 (m) REVERT: D 216 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7853 (ttmm) REVERT: D 264 GLU cc_start: 0.7375 (mp0) cc_final: 0.7165 (mp0) REVERT: D 277 GLU cc_start: 0.8232 (tt0) cc_final: 0.7972 (tp30) REVERT: D 281 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6981 (ttm-80) REVERT: D 331 VAL cc_start: 0.8382 (t) cc_final: 0.7998 (p) REVERT: D 364 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7401 (mt-10) REVERT: D 365 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6939 (tm-30) REVERT: D 380 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: D 578 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 602 VAL cc_start: 0.8102 (m) cc_final: 0.7846 (p) REVERT: D 610 GLN cc_start: 0.7857 (mm110) cc_final: 0.7616 (mm110) REVERT: D 637 ILE cc_start: 0.8250 (pt) cc_final: 0.8016 (mt) REVERT: D 657 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: D 750 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7683 (mtt180) REVERT: D 785 ASP cc_start: 0.8079 (t0) cc_final: 0.7809 (t0) REVERT: D 787 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7536 (mm-30) REVERT: D 791 MET cc_start: 0.8795 (tmm) cc_final: 0.8576 (ttp) REVERT: D 918 GLN cc_start: 0.7356 (tp-100) cc_final: 0.7119 (tp-100) REVERT: D 923 ASN cc_start: 0.7796 (m-40) cc_final: 0.7588 (m-40) REVERT: D 972 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8387 (mtpp) REVERT: D 982 ILE cc_start: 0.8433 (mm) cc_final: 0.8134 (mp) REVERT: D 1025 ASP cc_start: 0.8258 (t70) cc_final: 0.7179 (t0) REVERT: D 1075 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: D 1077 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6475 (mp0) outliers start: 76 outliers final: 46 residues processed: 516 average time/residue: 0.6491 time to fit residues: 370.1805 Evaluate side-chains 522 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 464 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1407 THR Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A1015 GLN A1124 GLN B 171 GLN B1290 ASN ** B1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 220 GLN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 254 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 845 GLN ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119117 restraints weight = 23680.534| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.82 r_work: 0.3239 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18121 Z= 0.260 Angle : 0.700 14.442 24639 Z= 0.356 Chirality : 0.045 0.279 2873 Planarity : 0.004 0.064 2905 Dihedral : 17.105 171.442 2873 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 4.41 % Allowed : 21.60 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2032 helix: 2.32 (0.14), residues: 1282 sheet: 1.28 (0.40), residues: 169 loop : -1.16 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1400 TYR 0.027 0.002 TYR B 326 PHE 0.026 0.002 PHE B1388 TRP 0.021 0.002 TRP C 49 HIS 0.014 0.002 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00619 (18121) covalent geometry : angle 0.70027 (24639) hydrogen bonds : bond 0.05487 ( 1138) hydrogen bonds : angle 4.13697 ( 3317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 492 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7811 (pt0) cc_final: 0.7467 (pt0) REVERT: A 20 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 53 SER cc_start: 0.8648 (t) cc_final: 0.8226 (p) REVERT: A 90 ASN cc_start: 0.7338 (t0) cc_final: 0.6944 (t0) REVERT: A 100 GLN cc_start: 0.7546 (tp-100) cc_final: 0.6705 (tp40) REVERT: A 114 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8370 (mmmm) REVERT: A 187 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8171 (ttmm) REVERT: A 209 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7865 (mttt) REVERT: A 1009 LYS cc_start: 0.8263 (mttt) cc_final: 0.7956 (mtmm) REVERT: A 1027 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 1067 LEU cc_start: 0.8441 (mp) cc_final: 0.8052 (mt) REVERT: A 1082 ILE cc_start: 0.8574 (pt) cc_final: 0.8363 (mm) REVERT: A 1108 MET cc_start: 0.8506 (ptp) cc_final: 0.8272 (ptp) REVERT: B 138 GLN cc_start: 0.7543 (mm110) cc_final: 0.7196 (mm110) REVERT: B 139 LYS cc_start: 0.7606 (mttt) cc_final: 0.7375 (mtmt) REVERT: B 170 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8240 (ttpp) REVERT: B 209 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8228 (mtp) REVERT: B 274 GLU cc_start: 0.7740 (mp0) cc_final: 0.7484 (mp0) REVERT: B 284 LYS cc_start: 0.8270 (ttmt) cc_final: 0.8021 (ttmm) REVERT: B 317 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7686 (pmmt) REVERT: B 325 GLU cc_start: 0.7735 (mp0) cc_final: 0.7313 (mp0) REVERT: B 335 ASN cc_start: 0.7606 (m-40) cc_final: 0.7346 (m-40) REVERT: B 1254 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.4878 (mp0) REVERT: B 1264 PHE cc_start: 0.7910 (t80) cc_final: 0.7604 (t80) REVERT: B 1281 MET cc_start: 0.8869 (tpp) cc_final: 0.8589 (tpp) REVERT: B 1290 ASN cc_start: 0.8496 (m-40) cc_final: 0.8286 (m-40) REVERT: B 1295 LEU cc_start: 0.8403 (mm) cc_final: 0.8175 (mp) REVERT: B 1309 SER cc_start: 0.8867 (m) cc_final: 0.8638 (m) REVERT: B 1320 ILE cc_start: 0.8301 (mm) cc_final: 0.8092 (mm) REVERT: B 1410 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7899 (mttm) REVERT: C 30 ASN cc_start: 0.7967 (m-40) cc_final: 0.7706 (m-40) REVERT: C 80 ASP cc_start: 0.7555 (m-30) cc_final: 0.7329 (m-30) REVERT: C 87 SER cc_start: 0.8409 (m) cc_final: 0.8179 (p) REVERT: C 211 ASP cc_start: 0.7998 (t0) cc_final: 0.7783 (t0) REVERT: C 281 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7603 (mt) REVERT: C 285 MET cc_start: 0.7889 (mmm) cc_final: 0.7595 (mmm) REVERT: C 637 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8127 (m) REVERT: C 664 GLU cc_start: 0.7801 (tp30) cc_final: 0.7518 (tp30) REVERT: C 708 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 114 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7795 (mt-10) REVERT: D 115 TYR cc_start: 0.8636 (m-80) cc_final: 0.8302 (m-80) REVERT: D 120 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7806 (tm130) REVERT: D 163 GLN cc_start: 0.8200 (pt0) cc_final: 0.7916 (pt0) REVERT: D 166 ASN cc_start: 0.8096 (m110) cc_final: 0.7715 (m110) REVERT: D 211 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7913 (mptm) REVERT: D 217 MET cc_start: 0.8248 (tpt) cc_final: 0.8006 (tpt) REVERT: D 226 CYS cc_start: 0.8429 (m) cc_final: 0.8126 (m) REVERT: D 264 GLU cc_start: 0.7544 (mp0) cc_final: 0.7320 (mp0) REVERT: D 277 GLU cc_start: 0.8246 (tt0) cc_final: 0.7990 (tp30) REVERT: D 281 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6965 (ttm-80) REVERT: D 313 MET cc_start: 0.8456 (tpt) cc_final: 0.8233 (OUTLIER) REVERT: D 364 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7543 (mt-10) REVERT: D 365 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6963 (tm-30) REVERT: D 380 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: D 578 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7395 (mm-30) REVERT: D 657 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: D 785 ASP cc_start: 0.8167 (t0) cc_final: 0.7915 (t0) REVERT: D 787 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7553 (mm-30) REVERT: D 791 MET cc_start: 0.8824 (tmm) cc_final: 0.8581 (ttp) REVERT: D 872 LYS cc_start: 0.7844 (tttm) cc_final: 0.7525 (ttpp) REVERT: D 972 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8417 (mtpp) REVERT: D 982 ILE cc_start: 0.8502 (mm) cc_final: 0.8215 (mp) REVERT: D 1025 ASP cc_start: 0.8315 (t70) cc_final: 0.7357 (m-30) REVERT: D 1075 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: D 1077 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: D 1126 GLN cc_start: 0.7649 (tt0) cc_final: 0.7251 (tt0) outliers start: 83 outliers final: 47 residues processed: 539 average time/residue: 0.6418 time to fit residues: 383.4910 Evaluate side-chains 536 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 478 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 1022 ARG Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 44 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 190 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 169 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 132 GLN A 137 ASN A 193 GLN A1075 ASN B 132 ASN B1385 ASN D 72 GLN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 845 GLN D1010 ASN ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123633 restraints weight = 23756.584| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.75 r_work: 0.3314 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18121 Z= 0.129 Angle : 0.607 10.406 24639 Z= 0.312 Chirality : 0.040 0.284 2873 Planarity : 0.004 0.047 2905 Dihedral : 17.023 174.373 2873 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 3.24 % Allowed : 23.57 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 2032 helix: 2.45 (0.14), residues: 1294 sheet: 1.44 (0.41), residues: 170 loop : -1.03 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1400 TYR 0.021 0.001 TYR B 326 PHE 0.020 0.001 PHE B1388 TRP 0.015 0.001 TRP C 49 HIS 0.014 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00281 (18121) covalent geometry : angle 0.60695 (24639) hydrogen bonds : bond 0.04245 ( 1138) hydrogen bonds : angle 3.89309 ( 3317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 469 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7756 (pt0) cc_final: 0.7481 (pt0) REVERT: A 20 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 53 SER cc_start: 0.8615 (t) cc_final: 0.8184 (p) REVERT: A 63 GLN cc_start: 0.8637 (tt0) cc_final: 0.8410 (tt0) REVERT: A 90 ASN cc_start: 0.7251 (t0) cc_final: 0.6913 (t0) REVERT: A 100 GLN cc_start: 0.7431 (tp-100) cc_final: 0.6723 (tp40) REVERT: A 108 VAL cc_start: 0.8008 (t) cc_final: 0.7732 (p) REVERT: A 1009 LYS cc_start: 0.8240 (mttt) cc_final: 0.7908 (mtmm) REVERT: A 1027 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 1067 LEU cc_start: 0.8431 (mp) cc_final: 0.8097 (mt) REVERT: A 1108 MET cc_start: 0.8452 (ptp) cc_final: 0.8230 (ptp) REVERT: B 138 GLN cc_start: 0.7539 (mm110) cc_final: 0.7223 (mm110) REVERT: B 139 LYS cc_start: 0.7513 (mttt) cc_final: 0.7291 (mtmt) REVERT: B 170 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8193 (ttpp) REVERT: B 274 GLU cc_start: 0.7648 (mp0) cc_final: 0.7402 (mp0) REVERT: B 292 ASP cc_start: 0.7737 (t70) cc_final: 0.7221 (t70) REVERT: B 325 GLU cc_start: 0.7711 (mp0) cc_final: 0.7202 (mp0) REVERT: B 335 ASN cc_start: 0.7491 (m-40) cc_final: 0.7259 (m-40) REVERT: B 1254 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.4894 (mp0) REVERT: B 1264 PHE cc_start: 0.7807 (t80) cc_final: 0.7470 (t80) REVERT: B 1281 MET cc_start: 0.8747 (tpp) cc_final: 0.8448 (tpp) REVERT: B 1408 THR cc_start: 0.8389 (m) cc_final: 0.8146 (m) REVERT: B 1410 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7804 (mttm) REVERT: C 30 ASN cc_start: 0.7702 (m-40) cc_final: 0.7368 (m-40) REVERT: C 63 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.6981 (pp) REVERT: C 80 ASP cc_start: 0.7491 (m-30) cc_final: 0.7197 (m-30) REVERT: C 171 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7280 (mm-30) REVERT: C 211 ASP cc_start: 0.7808 (t0) cc_final: 0.7597 (t0) REVERT: C 664 GLU cc_start: 0.7695 (tp30) cc_final: 0.7471 (tp30) REVERT: C 708 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8182 (mm) REVERT: C 738 ASN cc_start: 0.8595 (m-40) cc_final: 0.8360 (m-40) REVERT: D 114 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7555 (mt-10) REVERT: D 115 TYR cc_start: 0.8627 (m-80) cc_final: 0.8265 (m-80) REVERT: D 120 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7725 (tm130) REVERT: D 163 GLN cc_start: 0.8152 (pt0) cc_final: 0.7791 (pt0) REVERT: D 166 ASN cc_start: 0.8042 (m110) cc_final: 0.7653 (m110) REVERT: D 183 PHE cc_start: 0.8795 (m-80) cc_final: 0.8262 (m-80) REVERT: D 216 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7796 (tttm) REVERT: D 259 LYS cc_start: 0.8290 (tttm) cc_final: 0.7976 (tptt) REVERT: D 331 VAL cc_start: 0.8347 (t) cc_final: 0.8017 (p) REVERT: D 364 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 365 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7000 (tm-30) REVERT: D 380 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: D 578 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7259 (mm-30) REVERT: D 785 ASP cc_start: 0.8084 (t0) cc_final: 0.7815 (t0) REVERT: D 787 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7505 (mm-30) REVERT: D 791 MET cc_start: 0.8731 (tmm) cc_final: 0.8506 (ttp) REVERT: D 972 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8405 (mtpp) REVERT: D 982 ILE cc_start: 0.8448 (mm) cc_final: 0.8127 (mp) REVERT: D 1025 ASP cc_start: 0.8259 (t70) cc_final: 0.7115 (t0) REVERT: D 1075 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: D 1077 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: D 1126 GLN cc_start: 0.7636 (tt0) cc_final: 0.7249 (tt0) outliers start: 61 outliers final: 28 residues processed: 499 average time/residue: 0.6555 time to fit residues: 360.9996 Evaluate side-chains 501 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 465 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 199 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 171 GLN B1385 ASN D 111 HIS D 127 GLN D 178 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123549 restraints weight = 23756.654| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.77 r_work: 0.3314 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18121 Z= 0.133 Angle : 0.621 10.468 24639 Z= 0.318 Chirality : 0.040 0.309 2873 Planarity : 0.004 0.075 2905 Dihedral : 16.977 173.552 2873 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 24.63 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.19), residues: 2032 helix: 2.48 (0.14), residues: 1293 sheet: 1.42 (0.41), residues: 171 loop : -0.96 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1400 TYR 0.020 0.001 TYR B 326 PHE 0.020 0.001 PHE B1388 TRP 0.014 0.001 TRP C 49 HIS 0.016 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00297 (18121) covalent geometry : angle 0.62119 (24639) hydrogen bonds : bond 0.04258 ( 1138) hydrogen bonds : angle 3.89486 ( 3317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 474 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7771 (pt0) cc_final: 0.7490 (pt0) REVERT: A 20 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7835 (mt) REVERT: A 53 SER cc_start: 0.8605 (t) cc_final: 0.8168 (p) REVERT: A 78 SER cc_start: 0.8223 (t) cc_final: 0.8013 (p) REVERT: A 90 ASN cc_start: 0.7250 (t0) cc_final: 0.6926 (t0) REVERT: A 100 GLN cc_start: 0.7461 (tp-100) cc_final: 0.6759 (tp40) REVERT: A 108 VAL cc_start: 0.7987 (t) cc_final: 0.7733 (p) REVERT: A 216 MET cc_start: 0.7380 (mmm) cc_final: 0.6869 (mmm) REVERT: A 1009 LYS cc_start: 0.8230 (mttt) cc_final: 0.7892 (mtmm) REVERT: A 1027 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 1075 ASN cc_start: 0.8427 (m-40) cc_final: 0.8213 (m110) REVERT: A 1108 MET cc_start: 0.8431 (ptp) cc_final: 0.8206 (ptp) REVERT: B 138 GLN cc_start: 0.7553 (mm110) cc_final: 0.7232 (mm110) REVERT: B 139 LYS cc_start: 0.7508 (mttt) cc_final: 0.7288 (mtmt) REVERT: B 209 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: B 274 GLU cc_start: 0.7660 (mp0) cc_final: 0.7410 (mp0) REVERT: B 292 ASP cc_start: 0.7693 (t70) cc_final: 0.7233 (t70) REVERT: B 325 GLU cc_start: 0.7721 (mp0) cc_final: 0.7202 (mp0) REVERT: B 335 ASN cc_start: 0.7491 (m-40) cc_final: 0.7265 (m-40) REVERT: B 1254 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.4967 (mp0) REVERT: B 1264 PHE cc_start: 0.7828 (t80) cc_final: 0.7485 (t80) REVERT: B 1271 PHE cc_start: 0.8082 (t80) cc_final: 0.7724 (t80) REVERT: B 1281 MET cc_start: 0.8739 (tpp) cc_final: 0.8442 (tpp) REVERT: B 1408 THR cc_start: 0.8390 (m) cc_final: 0.8138 (m) REVERT: C 30 ASN cc_start: 0.7617 (m-40) cc_final: 0.7264 (m110) REVERT: C 63 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6990 (pp) REVERT: C 80 ASP cc_start: 0.7443 (m-30) cc_final: 0.7242 (m-30) REVERT: C 171 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 211 ASP cc_start: 0.7857 (t0) cc_final: 0.7626 (t0) REVERT: C 664 GLU cc_start: 0.7752 (tp30) cc_final: 0.7510 (tp30) REVERT: C 708 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8139 (mt) REVERT: D 86 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7864 (mtmm) REVERT: D 114 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7765 (mt-10) REVERT: D 115 TYR cc_start: 0.8630 (m-80) cc_final: 0.8270 (m-80) REVERT: D 120 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7720 (tm130) REVERT: D 163 GLN cc_start: 0.8109 (pt0) cc_final: 0.7732 (pt0) REVERT: D 166 ASN cc_start: 0.8066 (m110) cc_final: 0.7750 (m110) REVERT: D 183 PHE cc_start: 0.8777 (m-80) cc_final: 0.8267 (m-80) REVERT: D 216 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7819 (tttm) REVERT: D 241 MET cc_start: 0.8463 (mmp) cc_final: 0.8231 (mmm) REVERT: D 315 LEU cc_start: 0.8152 (pp) cc_final: 0.7944 (pp) REVERT: D 331 VAL cc_start: 0.8340 (t) cc_final: 0.8016 (p) REVERT: D 364 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7265 (mt-10) REVERT: D 365 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 380 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: D 429 HIS cc_start: 0.8224 (p90) cc_final: 0.7815 (p-80) REVERT: D 578 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 785 ASP cc_start: 0.8093 (t0) cc_final: 0.7813 (t0) REVERT: D 787 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7518 (mm-30) REVERT: D 791 MET cc_start: 0.8746 (tmm) cc_final: 0.8527 (ttp) REVERT: D 972 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8428 (mtpp) REVERT: D 982 ILE cc_start: 0.8455 (mm) cc_final: 0.8112 (mp) REVERT: D 1025 ASP cc_start: 0.8280 (t70) cc_final: 0.7301 (m-30) REVERT: D 1073 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6008 (tt) REVERT: D 1075 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: D 1077 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: D 1126 GLN cc_start: 0.7634 (tt0) cc_final: 0.7232 (tt0) outliers start: 51 outliers final: 28 residues processed: 502 average time/residue: 0.6570 time to fit residues: 365.1053 Evaluate side-chains 509 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 471 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1073 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 175 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 140 ASN A 193 GLN A1042 ASN B 171 GLN B1272 ASN ** B1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN D 111 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120815 restraints weight = 23868.971| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.80 r_work: 0.3265 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18121 Z= 0.197 Angle : 0.670 11.080 24639 Z= 0.342 Chirality : 0.043 0.310 2873 Planarity : 0.004 0.068 2905 Dihedral : 16.999 171.964 2873 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.65 % Allowed : 24.95 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2032 helix: 2.34 (0.14), residues: 1289 sheet: 1.41 (0.41), residues: 170 loop : -1.08 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1400 TYR 0.025 0.002 TYR B 326 PHE 0.023 0.002 PHE D 196 TRP 0.019 0.002 TRP C 49 HIS 0.017 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00467 (18121) covalent geometry : angle 0.66999 (24639) hydrogen bonds : bond 0.04925 ( 1138) hydrogen bonds : angle 4.05085 ( 3317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8144.54 seconds wall clock time: 138 minutes 54.81 seconds (8334.81 seconds total)