Starting phenix.real_space_refine on Sat Jul 4 09:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf5_44490/07_2026/9bf5_44490.map" } resolution = 3.07 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 48 5.16 5 C 12402 2.51 5 N 3466 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19742 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 9600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9600 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1155} Chain: "D" Number of atoms: 9600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9600 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1155} Time building chain proxies: 4.43, per 1000 atoms: 0.22 Number of scatterers: 19742 At special positions: 0 Unit cell: (122.1, 148.74, 153.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 26 15.00 O 3800 8.00 N 3466 7.00 C 12402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 829.0 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 20 sheets defined 50.5% alpha, 9.3% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.595A pdb=" N PHE C 8 " --> pdb=" O ILE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.948A pdb=" N LEU C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 25 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 55 through 78 removed outlier: 3.541A pdb=" N ALA C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 111 removed outlier: 3.527A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.526A pdb=" N LEU C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 removed outlier: 3.539A pdb=" N GLN C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 207 removed outlier: 4.178A pdb=" N SER C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 227 removed outlier: 3.669A pdb=" N ALA C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 4.243A pdb=" N ARG C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.772A pdb=" N VAL C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.583A pdb=" N ASP C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 Processing helix chain 'C' and resid 322 through 337 removed outlier: 3.718A pdb=" N GLU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 435 removed outlier: 3.640A pdb=" N PHE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 435 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.657A pdb=" N VAL C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.650A pdb=" N GLU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 497 removed outlier: 3.740A pdb=" N HIS C 496 " --> pdb=" O SER C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.784A pdb=" N GLY C 536 " --> pdb=" O MET C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 removed outlier: 3.761A pdb=" N GLU C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 605 through 616 Processing helix chain 'C' and resid 621 through 629 removed outlier: 3.771A pdb=" N ILE C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 657 removed outlier: 3.578A pdb=" N SER C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 674 No H-bonds generated for 'chain 'C' and resid 672 through 674' Processing helix chain 'C' and resid 675 through 693 Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 713 through 721 removed outlier: 4.008A pdb=" N SER C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 738 removed outlier: 4.105A pdb=" N ALA C 738 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 808 removed outlier: 3.828A pdb=" N GLN C 794 " --> pdb=" O HIS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 Processing helix chain 'C' and resid 827 through 836 Processing helix chain 'C' and resid 839 through 855 removed outlier: 3.741A pdb=" N SER C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 879 Processing helix chain 'C' and resid 891 through 901 removed outlier: 3.799A pdb=" N SER C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.236A pdb=" N ARG C 913 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 938 " --> pdb=" O VAL C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 960 removed outlier: 3.853A pdb=" N ILE C 947 " --> pdb=" O SER C 943 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1002 No H-bonds generated for 'chain 'C' and resid 1000 through 1002' Processing helix chain 'C' and resid 1009 through 1014 removed outlier: 3.784A pdb=" N CYS C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1014 " --> pdb=" O GLU C1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1009 through 1014' Processing helix chain 'C' and resid 1014 through 1020 removed outlier: 3.539A pdb=" N GLN C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1031 Processing helix chain 'C' and resid 1045 through 1051 removed outlier: 3.582A pdb=" N THR C1050 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C1051 " --> pdb=" O ILE C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1069 removed outlier: 3.798A pdb=" N GLN C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C1068 " --> pdb=" O ALA C1064 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE C1069 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1127 removed outlier: 4.360A pdb=" N SER C1116 " --> pdb=" O SER C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1176 through 1187 removed outlier: 4.297A pdb=" N VAL C1180 " --> pdb=" O ASN C1176 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.738A pdb=" N GLU D 7 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 removed outlier: 4.218A pdb=" N THR D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 54 through 76 removed outlier: 3.543A pdb=" N LYS D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.649A pdb=" N LEU D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.532A pdb=" N LEU D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.646A pdb=" N ARG D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 207 Processing helix chain 'D' and resid 217 through 227 Processing helix chain 'D' and resid 229 through 235 removed outlier: 3.635A pdb=" N ARG D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 292 through 304 Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.725A pdb=" N ASP D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 321 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.513A pdb=" N TRP D 336 " --> pdb=" O PHE D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 395 removed outlier: 4.314A pdb=" N LEU D 395 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 434 removed outlier: 3.662A pdb=" N PHE D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 459 removed outlier: 3.681A pdb=" N PHE D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 471 through 476 Processing helix chain 'D' and resid 493 through 497 removed outlier: 3.690A pdb=" N HIS D 496 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 556 through 564 Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 604 through 616 removed outlier: 3.800A pdb=" N LEU D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 636 through 656 removed outlier: 4.078A pdb=" N VAL D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 650 " --> pdb=" O LYS D 646 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 656 " --> pdb=" O LYS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 674 No H-bonds generated for 'chain 'D' and resid 672 through 674' Processing helix chain 'D' and resid 675 through 693 removed outlier: 3.625A pdb=" N PHE D 693 " --> pdb=" O TRP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 709 Processing helix chain 'D' and resid 713 through 721 removed outlier: 4.052A pdb=" N SER D 717 " --> pdb=" O TYR D 713 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN D 721 " --> pdb=" O SER D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 738 Processing helix chain 'D' and resid 790 through 808 removed outlier: 3.764A pdb=" N GLN D 794 " --> pdb=" O HIS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 825 Processing helix chain 'D' and resid 827 through 836 removed outlier: 3.682A pdb=" N GLN D 834 " --> pdb=" O ARG D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 855 removed outlier: 3.755A pdb=" N SER D 843 " --> pdb=" O SER D 839 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 855 " --> pdb=" O GLN D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 879 removed outlier: 3.560A pdb=" N LYS D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 877 " --> pdb=" O GLY D 873 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 879 " --> pdb=" O LYS D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 901 removed outlier: 3.559A pdb=" N ALA D 894 " --> pdb=" O HIS D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 939 removed outlier: 4.205A pdb=" N ARG D 913 " --> pdb=" O ASP D 909 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 939 " --> pdb=" O HIS D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 960 Processing helix chain 'D' and resid 1000 through 1002 No H-bonds generated for 'chain 'D' and resid 1000 through 1002' Processing helix chain 'D' and resid 1024 through 1032 removed outlier: 3.556A pdb=" N PHE D1028 " --> pdb=" O VAL D1024 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D1029 " --> pdb=" O ARG D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1051 removed outlier: 3.766A pdb=" N THR D1050 " --> pdb=" O PRO D1046 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN D1051 " --> pdb=" O ILE D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1069 removed outlier: 3.745A pdb=" N PHE D1069 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 1111 through 1126 removed outlier: 3.672A pdb=" N TYR D1115 " --> pdb=" O SER D1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1189 removed outlier: 3.723A pdb=" N VAL D1180 " --> pdb=" O ASN D1176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 48 removed outlier: 5.720A pdb=" N ALA C 43 " --> pdb=" O ILE C 539 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLY C 541 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C 45 " --> pdb=" O GLY C 541 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N SER C 543 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 47 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 267 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 540 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU C 269 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C 542 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 271 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 87 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 270 " --> pdb=" O LEU C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AA3, first strand: chain 'C' and resid 342 through 344 removed outlier: 6.985A pdb=" N ASN C 343 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 382 " --> pdb=" O ASP C 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 364 through 366 removed outlier: 3.694A pdb=" N VAL C 354 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 358 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 521 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 505 " --> pdb=" O ASN C 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 595 through 601 removed outlier: 3.740A pdb=" N LYS C 599 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 870 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 601 " --> pdb=" O VAL C 870 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 774 " --> pdb=" O PHE C 869 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP C 871 " --> pdb=" O ILE C 774 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 773 " --> pdb=" O TYR C 662 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 731 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 730 " --> pdb=" O PHE C 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 744 through 745 removed outlier: 4.252A pdb=" N TYR C 744 " --> pdb=" O SER C 769 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 769 " --> pdb=" O TYR C 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 974 through 975 Processing sheet with id=AA8, first strand: chain 'C' and resid 997 through 998 removed outlier: 3.723A pdb=" N GLU C 997 " --> pdb=" O GLN C 986 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 983 " --> pdb=" O VAL C1008 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C1008 " --> pdb=" O TYR C 983 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1072 through 1074 removed outlier: 3.746A pdb=" N THR C1072 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C1089 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C1087 " --> pdb=" O GLU C1074 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C1086 " --> pdb=" O LEU C1099 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C1099 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C1097 " --> pdb=" O VAL C1088 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C1134 " --> pdb=" O ASP C1100 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C1162 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C1164 " --> pdb=" O TYR C1133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C1145 " --> pdb=" O GLU C1163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 47 removed outlier: 6.081A pdb=" N ALA D 43 " --> pdb=" O ILE D 539 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY D 541 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU D 45 " --> pdb=" O GLY D 541 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 88 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU D 242 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR D 90 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AB3, first strand: chain 'D' and resid 251 through 252 Processing sheet with id=AB4, first strand: chain 'D' and resid 341 through 344 removed outlier: 3.688A pdb=" N LYS D 382 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 386 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 364 through 366 removed outlier: 3.540A pdb=" N VAL D 354 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 358 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 521 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 505 " --> pdb=" O ASN D 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 595 through 600 removed outlier: 6.406A pdb=" N ILE D 774 " --> pdb=" O PHE D 869 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET D 663 " --> pdb=" O VAL D 729 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 731 " --> pdb=" O MET D 663 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER D 665 " --> pdb=" O SER D 731 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 730 " --> pdb=" O PHE D 700 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 756 through 757 removed outlier: 3.563A pdb=" N LYS D 862 " --> pdb=" O ILE D 756 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 974 through 975 Processing sheet with id=AB9, first strand: chain 'D' and resid 997 through 998 removed outlier: 3.569A pdb=" N GLU D 997 " --> pdb=" O GLN D 986 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 983 " --> pdb=" O VAL D1008 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1086 through 1090 removed outlier: 6.764A pdb=" N ASN D1086 " --> pdb=" O ILE D1097 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D1097 " --> pdb=" O ASN D1086 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL D1088 " --> pdb=" O GLN D1095 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN D1095 " --> pdb=" O VAL D1088 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE D1090 " --> pdb=" O ILE D1093 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LYS D1130 " --> pdb=" O GLU D1094 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE D1132 " --> pdb=" O PRO D1096 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP D1098 " --> pdb=" O ILE D1132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D1134 " --> pdb=" O TRP D1098 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP D1100 " --> pdb=" O VAL D1134 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D1162 " --> pdb=" O PHE D1131 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D1164 " --> pdb=" O TYR D1133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D1135 " --> pdb=" O ILE D1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1137 through 1138 removed outlier: 3.562A pdb=" N GLY D1138 " --> pdb=" O ILE D1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 825 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5063 1.33 - 1.45: 3949 1.45 - 1.57: 11058 1.57 - 1.69: 50 1.69 - 1.81: 76 Bond restraints: 20196 Sorted by residual: bond pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" C3' DT B 19 " pdb=" C2' DT B 19 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.46e+01 bond pdb=" C3' DG B 16 " pdb=" C2' DG B 16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT B 23 " pdb=" C2' DT B 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DG A 18 " pdb=" C2' DG A 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 ... (remaining 20191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 27319 2.89 - 5.77: 93 5.77 - 8.66: 1 8.66 - 11.54: 0 11.54 - 14.43: 1 Bond angle restraints: 27414 Sorted by residual: angle pdb=" N3 DT A 23 " pdb=" C4 DT A 23 " pdb=" O4 DT A 23 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" CA LEU D 612 " pdb=" CB LEU D 612 " pdb=" CG LEU D 612 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 angle pdb=" N3 DT A 12 " pdb=" C4 DT A 12 " pdb=" O4 DT A 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 23 " pdb=" C4 DT B 23 " pdb=" O4 DT B 23 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT A 19 " pdb=" C4 DT A 19 " pdb=" O4 DT A 19 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 ... (remaining 27409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10403 17.89 - 35.77: 1286 35.77 - 53.66: 326 53.66 - 71.55: 81 71.55 - 89.43: 18 Dihedral angle restraints: 12114 sinusoidal: 5122 harmonic: 6992 Sorted by residual: dihedral pdb=" CA VAL D 746 " pdb=" C VAL D 746 " pdb=" N ASN D 747 " pdb=" CA ASN D 747 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR C 780 " pdb=" C THR C 780 " pdb=" N GLN C 781 " pdb=" CA GLN C 781 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TYR D 744 " pdb=" C TYR D 744 " pdb=" N ALA D 745 " pdb=" CA ALA D 745 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1921 0.030 - 0.060: 739 0.060 - 0.090: 207 0.090 - 0.120: 127 0.120 - 0.150: 18 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA PHE D 684 " pdb=" N PHE D 684 " pdb=" C PHE D 684 " pdb=" CB PHE D 684 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CB ILE C1080 " pdb=" CA ILE C1080 " pdb=" CG1 ILE C1080 " pdb=" CG2 ILE C1080 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL C 695 " pdb=" N VAL C 695 " pdb=" C VAL C 695 " pdb=" CB VAL C 695 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3009 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 884 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" CG ASP C 884 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP C 884 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP C 884 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 312 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO D 313 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 313 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 313 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 884 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ASP C 884 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP C 884 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 885 " -0.012 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 340 2.68 - 3.24: 17780 3.24 - 3.79: 27674 3.79 - 4.35: 35733 4.35 - 4.90: 61595 Nonbonded interactions: 143122 Sorted by model distance: nonbonded pdb=" O ASN D 566 " pdb=" ND2 ASN D 566 " model vdw 2.131 3.120 nonbonded pdb=" CD1 LEU D1099 " pdb=" O ILE D1132 " model vdw 2.205 3.460 nonbonded pdb=" OG SER D 491 " pdb=" O GLU D 968 " model vdw 2.227 3.040 nonbonded pdb=" O ASN D 660 " pdb=" NZ LYS D 726 " model vdw 2.239 3.120 nonbonded pdb=" OD2 ASP D 93 " pdb=" NE2 GLN D 277 " model vdw 2.251 3.120 ... (remaining 143117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 23) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.640 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.059 20196 Z= 0.167 Angle : 0.513 14.427 27414 Z= 0.314 Chirality : 0.039 0.150 3012 Planarity : 0.004 0.051 3474 Dihedral : 16.898 89.433 7586 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.15 (0.18), residues: 2376 helix: 1.92 (0.16), residues: 1067 sheet: 0.05 (0.33), residues: 280 loop : -2.50 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 233 TYR 0.018 0.001 TYR D 413 PHE 0.027 0.001 PHE D 684 TRP 0.025 0.001 TRP C 643 HIS 0.008 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.17 (20196) covalent geometry : angle 0.51300 / 0.31 (27414) hydrogen bonds : bond 0.18299 / 18.19 ( 825) hydrogen bonds : angle 5.00101 / 4.58 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6210 (tm-30) REVERT: C 212 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8310 (ttm110) REVERT: C 272 ASP cc_start: 0.7061 (p0) cc_final: 0.6568 (p0) REVERT: C 327 GLU cc_start: 0.7843 (mp0) cc_final: 0.7444 (mp0) REVERT: C 345 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7180 (tm-30) REVERT: C 463 GLU cc_start: 0.8127 (pm20) cc_final: 0.7873 (pm20) REVERT: C 636 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 723 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7111 (tm-30) REVERT: C 817 ASN cc_start: 0.8303 (t0) cc_final: 0.7755 (t0) REVERT: C 861 LEU cc_start: 0.7722 (mt) cc_final: 0.7457 (mt) REVERT: C 943 SER cc_start: 0.7409 (t) cc_final: 0.7203 (t) REVERT: C 992 ASP cc_start: 0.7313 (t70) cc_final: 0.7077 (t70) REVERT: C 997 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7317 (mm-30) REVERT: D 50 GLN cc_start: 0.7168 (mt0) cc_final: 0.6850 (mt0) REVERT: D 69 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 470 GLU cc_start: 0.7201 (mp0) cc_final: 0.6966 (mp0) REVERT: D 561 ASN cc_start: 0.8514 (t0) cc_final: 0.8292 (t0) REVERT: D 605 ASP cc_start: 0.7917 (m-30) cc_final: 0.7586 (m-30) REVERT: D 837 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8551 (mm-40) REVERT: D 952 ASP cc_start: 0.7856 (m-30) cc_final: 0.7345 (m-30) REVERT: D 970 PHE cc_start: 0.7622 (m-10) cc_final: 0.7273 (m-80) REVERT: D 980 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7674 (ttmm) REVERT: D 997 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 1012 ASP cc_start: 0.8105 (m-30) cc_final: 0.7863 (m-30) REVERT: D 1059 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6951 (mt-10) REVERT: D 1085 ASP cc_start: 0.7272 (t0) cc_final: 0.6334 (t0) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1802 time to fit residues: 87.7261 Evaluate side-chains 333 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 GLN C 938 HIS D 204 GLN D 458 HIS D 566 ASN D 865 GLN D 939 ASN D1181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124062 restraints weight = 28236.544| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.43 r_work: 0.3418 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20196 Z= 0.198 Angle : 0.570 9.860 27414 Z= 0.311 Chirality : 0.042 0.171 3012 Planarity : 0.004 0.051 3474 Dihedral : 10.857 87.095 2888 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.80 % Allowed : 11.97 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.22 (0.17), residues: 2376 helix: 1.77 (0.16), residues: 1080 sheet: 0.14 (0.31), residues: 282 loop : -2.51 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.019 0.002 TYR D 413 PHE 0.021 0.002 PHE D 684 TRP 0.027 0.001 TRP C 643 HIS 0.009 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (20196) covalent geometry : angle 0.57003 / 0.31 (27414) hydrogen bonds : bond 0.07392 / 7.40 ( 825) hydrogen bonds : angle 4.25719 / 3.81 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6518 (tm-30) REVERT: C 183 GLU cc_start: 0.6864 (pm20) cc_final: 0.6138 (pm20) REVERT: C 212 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8463 (ttm110) REVERT: C 272 ASP cc_start: 0.7475 (p0) cc_final: 0.7040 (p0) REVERT: C 323 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6371 (mt-10) REVERT: C 327 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 345 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 463 GLU cc_start: 0.8429 (pm20) cc_final: 0.8185 (pm20) REVERT: C 583 TYR cc_start: 0.6453 (t80) cc_final: 0.5924 (t80) REVERT: C 607 PHE cc_start: 0.7624 (t80) cc_final: 0.7360 (t80) REVERT: C 636 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 861 LEU cc_start: 0.7776 (mt) cc_final: 0.7522 (mt) REVERT: C 943 SER cc_start: 0.7539 (t) cc_final: 0.7320 (t) REVERT: C 992 ASP cc_start: 0.7601 (t70) cc_final: 0.7290 (t70) REVERT: C 1063 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 1142 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8141 (mmtt) REVERT: D 50 GLN cc_start: 0.7464 (mt0) cc_final: 0.7042 (mt0) REVERT: D 69 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 108 LEU cc_start: 0.7895 (tp) cc_final: 0.7676 (tp) REVERT: D 275 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.5521 (m-30) REVERT: D 289 GLN cc_start: 0.8001 (mm110) cc_final: 0.7777 (mm-40) REVERT: D 319 GLU cc_start: 0.7938 (tp30) cc_final: 0.7549 (tp30) REVERT: D 470 GLU cc_start: 0.7434 (mp0) cc_final: 0.7152 (mp0) REVERT: D 561 ASN cc_start: 0.8566 (t0) cc_final: 0.8355 (t0) REVERT: D 566 ASN cc_start: 0.8165 (t0) cc_final: 0.7958 (t0) REVERT: D 605 ASP cc_start: 0.8100 (m-30) cc_final: 0.7773 (m-30) REVERT: D 952 ASP cc_start: 0.8027 (m-30) cc_final: 0.7500 (m-30) REVERT: D 970 PHE cc_start: 0.7932 (m-10) cc_final: 0.7524 (m-80) REVERT: D 980 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7890 (ttmm) REVERT: D 982 TYR cc_start: 0.8518 (p90) cc_final: 0.8202 (p90) REVERT: D 997 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7366 (mm-30) REVERT: D 1012 ASP cc_start: 0.8262 (m-30) cc_final: 0.8028 (m-30) REVERT: D 1059 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7390 (mt-10) REVERT: D 1085 ASP cc_start: 0.7461 (t0) cc_final: 0.6616 (t0) REVERT: D 1124 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 38 outliers final: 25 residues processed: 362 average time/residue: 0.1766 time to fit residues: 93.1566 Evaluate side-chains 368 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 340 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 0.0980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 154 optimal weight: 0.3980 chunk 201 optimal weight: 0.5980 chunk 116 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 289 GLN C 522 ASN C 668 ASN C1176 ASN D 865 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125034 restraints weight = 28456.456| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.51 r_work: 0.3435 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20196 Z= 0.130 Angle : 0.502 9.684 27414 Z= 0.277 Chirality : 0.039 0.164 3012 Planarity : 0.003 0.046 3474 Dihedral : 10.710 86.452 2888 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.99 % Allowed : 13.11 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.09 (0.17), residues: 2376 helix: 1.90 (0.16), residues: 1090 sheet: 0.19 (0.31), residues: 279 loop : -2.52 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 233 TYR 0.012 0.001 TYR D 662 PHE 0.023 0.001 PHE D 684 TRP 0.026 0.001 TRP C 643 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (20196) covalent geometry : angle 0.50190 / 0.28 (27414) hydrogen bonds : bond 0.06141 / 6.14 ( 825) hydrogen bonds : angle 4.02715 / 3.60 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6655 (tm-30) cc_final: 0.6281 (tm-30) REVERT: C 272 ASP cc_start: 0.6986 (p0) cc_final: 0.6578 (p0) REVERT: C 323 GLU cc_start: 0.6301 (mt-10) cc_final: 0.5684 (mt-10) REVERT: C 327 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: C 345 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 463 GLU cc_start: 0.8165 (pm20) cc_final: 0.7960 (pm20) REVERT: C 583 TYR cc_start: 0.6196 (t80) cc_final: 0.5715 (t80) REVERT: C 586 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6968 (mmm-85) REVERT: C 636 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 723 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7112 (tm-30) REVERT: C 861 LEU cc_start: 0.7729 (mt) cc_final: 0.7463 (mt) REVERT: C 943 SER cc_start: 0.7388 (t) cc_final: 0.7177 (t) REVERT: C 992 ASP cc_start: 0.7283 (t70) cc_final: 0.7017 (t70) REVERT: C 1063 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 1142 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8120 (mmtt) REVERT: D 50 GLN cc_start: 0.7173 (mt0) cc_final: 0.6837 (mt0) REVERT: D 69 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 275 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.5012 (m-30) REVERT: D 289 GLN cc_start: 0.7782 (mm110) cc_final: 0.7543 (mm-40) REVERT: D 566 ASN cc_start: 0.8009 (t0) cc_final: 0.7793 (t0) REVERT: D 601 LEU cc_start: 0.8485 (mp) cc_final: 0.8277 (mt) REVERT: D 605 ASP cc_start: 0.7955 (m-30) cc_final: 0.7647 (m-30) REVERT: D 636 GLU cc_start: 0.7222 (pm20) cc_final: 0.6632 (pm20) REVERT: D 695 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7652 (m) REVERT: D 952 ASP cc_start: 0.7889 (m-30) cc_final: 0.7357 (m-30) REVERT: D 980 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7716 (ttmm) REVERT: D 982 TYR cc_start: 0.8358 (p90) cc_final: 0.8020 (p90) REVERT: D 997 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7084 (mm-30) REVERT: D 1012 ASP cc_start: 0.8127 (m-30) cc_final: 0.7906 (m-30) REVERT: D 1124 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7412 (mp0) outliers start: 42 outliers final: 26 residues processed: 355 average time/residue: 0.1804 time to fit residues: 92.7639 Evaluate side-chains 364 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 334 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 37 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 160 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 307 HIS C 486 ASN C 938 HIS D 865 GLN D 951 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122963 restraints weight = 28393.162| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.49 r_work: 0.3401 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20196 Z= 0.188 Angle : 0.546 9.764 27414 Z= 0.297 Chirality : 0.041 0.173 3012 Planarity : 0.004 0.048 3474 Dihedral : 10.799 86.000 2888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.42 % Allowed : 14.25 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.15 (0.17), residues: 2376 helix: 1.87 (0.16), residues: 1075 sheet: 0.14 (0.31), residues: 282 loop : -2.52 (0.17), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 661 TYR 0.017 0.002 TYR D 788 PHE 0.021 0.002 PHE D 684 TRP 0.028 0.001 TRP C 643 HIS 0.009 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (20196) covalent geometry : angle 0.54590 / 0.30 (27414) hydrogen bonds : bond 0.07346 / 7.33 ( 825) hydrogen bonds : angle 4.09494 / 3.66 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6778 (pm20) cc_final: 0.6326 (pm20) REVERT: C 272 ASP cc_start: 0.6976 (p0) cc_final: 0.6613 (p0) REVERT: C 323 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6045 (mt-10) REVERT: C 327 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: C 345 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 463 GLU cc_start: 0.8216 (pm20) cc_final: 0.7998 (pm20) REVERT: C 583 TYR cc_start: 0.6238 (t80) cc_final: 0.5766 (t80) REVERT: C 636 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7382 (mt-10) REVERT: C 723 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7121 (tm-30) REVERT: C 861 LEU cc_start: 0.7750 (mt) cc_final: 0.7507 (mt) REVERT: C 943 SER cc_start: 0.7382 (t) cc_final: 0.7163 (t) REVERT: C 992 ASP cc_start: 0.7288 (t70) cc_final: 0.7004 (t70) REVERT: C 1063 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 1142 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8142 (mmtt) REVERT: D 50 GLN cc_start: 0.7206 (mt0) cc_final: 0.6848 (mt0) REVERT: D 69 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 275 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.5187 (m-30) REVERT: D 289 GLN cc_start: 0.7773 (mm110) cc_final: 0.7541 (mm-40) REVERT: D 566 ASN cc_start: 0.8085 (t0) cc_final: 0.7826 (t0) REVERT: D 605 ASP cc_start: 0.7993 (m-30) cc_final: 0.7672 (m-30) REVERT: D 636 GLU cc_start: 0.7201 (pm20) cc_final: 0.6591 (pm20) REVERT: D 952 ASP cc_start: 0.7945 (m-30) cc_final: 0.7401 (m-30) REVERT: D 980 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7769 (ttmm) REVERT: D 982 TYR cc_start: 0.8371 (p90) cc_final: 0.7979 (p90) REVERT: D 997 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7043 (mm-30) REVERT: D 1012 ASP cc_start: 0.8162 (m-30) cc_final: 0.7930 (m-30) REVERT: D 1124 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7428 (mp0) outliers start: 51 outliers final: 38 residues processed: 366 average time/residue: 0.1703 time to fit residues: 90.7647 Evaluate side-chains 380 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 339 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 ASN D 865 GLN D1181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123908 restraints weight = 28123.364| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.47 r_work: 0.3413 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20196 Z= 0.154 Angle : 0.517 11.268 27414 Z= 0.283 Chirality : 0.040 0.168 3012 Planarity : 0.004 0.046 3474 Dihedral : 10.775 85.755 2888 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.85 % Allowed : 14.15 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.12 (0.17), residues: 2376 helix: 1.91 (0.16), residues: 1081 sheet: 0.16 (0.31), residues: 283 loop : -2.54 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.014 0.001 TYR D 788 PHE 0.023 0.001 PHE D 684 TRP 0.028 0.001 TRP C 643 HIS 0.006 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (20196) covalent geometry : angle 0.51743 / 0.28 (27414) hydrogen bonds : bond 0.06645 / 6.63 ( 825) hydrogen bonds : angle 3.99184 / 3.56 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6690 (pm20) cc_final: 0.6107 (pm20) REVERT: C 272 ASP cc_start: 0.6956 (p0) cc_final: 0.6600 (p0) REVERT: C 323 GLU cc_start: 0.6417 (mt-10) cc_final: 0.5930 (mt-10) REVERT: C 327 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: C 345 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7180 (tm-30) REVERT: C 463 GLU cc_start: 0.8188 (pm20) cc_final: 0.7979 (pm20) REVERT: C 583 TYR cc_start: 0.6229 (t80) cc_final: 0.5772 (t80) REVERT: C 586 ARG cc_start: 0.7312 (mmm160) cc_final: 0.6978 (mmm-85) REVERT: C 636 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 723 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 861 LEU cc_start: 0.7752 (mt) cc_final: 0.7488 (mt) REVERT: C 943 SER cc_start: 0.7362 (t) cc_final: 0.7136 (t) REVERT: C 992 ASP cc_start: 0.7274 (t70) cc_final: 0.6988 (t70) REVERT: C 1001 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6985 (mtt90) REVERT: C 1063 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 1142 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8133 (mmtt) REVERT: D 50 GLN cc_start: 0.7190 (mt0) cc_final: 0.6844 (mt0) REVERT: D 69 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 275 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.4984 (m-30) REVERT: D 566 ASN cc_start: 0.8076 (t0) cc_final: 0.7862 (t0) REVERT: D 605 ASP cc_start: 0.7989 (m-30) cc_final: 0.7680 (m-30) REVERT: D 636 GLU cc_start: 0.7255 (pm20) cc_final: 0.6783 (pm20) REVERT: D 695 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7634 (m) REVERT: D 952 ASP cc_start: 0.7934 (m-30) cc_final: 0.7394 (m-30) REVERT: D 980 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7763 (ttmm) REVERT: D 982 TYR cc_start: 0.8373 (p90) cc_final: 0.7894 (p90) REVERT: D 997 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7016 (mm-30) REVERT: D 1012 ASP cc_start: 0.8154 (m-30) cc_final: 0.7928 (m-30) REVERT: D 1124 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7445 (mp0) outliers start: 60 outliers final: 40 residues processed: 366 average time/residue: 0.1758 time to fit residues: 93.0570 Evaluate side-chains 381 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 627 ASN Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 706 ASP Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 137 optimal weight: 0.0370 chunk 228 optimal weight: 0.9990 chunk 63 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 197 optimal weight: 0.1980 chunk 38 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 ASN C 668 ASN D 865 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126613 restraints weight = 28039.032| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.42 r_work: 0.3454 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20196 Z= 0.110 Angle : 0.478 12.423 27414 Z= 0.262 Chirality : 0.038 0.171 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.671 85.773 2888 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.61 % Allowed : 14.81 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.08 (0.17), residues: 2376 helix: 2.13 (0.16), residues: 1078 sheet: 0.23 (0.31), residues: 291 loop : -2.50 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 233 TYR 0.010 0.001 TYR D 615 PHE 0.024 0.001 PHE D 684 TRP 0.025 0.001 TRP C 643 HIS 0.003 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (20196) covalent geometry : angle 0.47758 / 0.26 (27414) hydrogen bonds : bond 0.05229 / 5.23 ( 825) hydrogen bonds : angle 3.76441 / 3.36 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 336 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6244 (tm-30) REVERT: C 183 GLU cc_start: 0.6626 (pm20) cc_final: 0.6281 (pm20) REVERT: C 272 ASP cc_start: 0.6948 (p0) cc_final: 0.6642 (p0) REVERT: C 327 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: C 345 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7154 (tm-30) REVERT: C 463 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: C 583 TYR cc_start: 0.6158 (t80) cc_final: 0.5700 (t80) REVERT: C 586 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6823 (mmm-85) REVERT: C 636 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7350 (mt-10) REVERT: C 723 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 861 LEU cc_start: 0.7690 (mt) cc_final: 0.7444 (mt) REVERT: C 943 SER cc_start: 0.7274 (t) cc_final: 0.7041 (t) REVERT: C 992 ASP cc_start: 0.7295 (t70) cc_final: 0.6983 (t70) REVERT: C 1001 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6982 (mtt90) REVERT: C 1029 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: C 1063 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7242 (tm-30) REVERT: C 1142 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8089 (mmtt) REVERT: D 50 GLN cc_start: 0.7186 (mt0) cc_final: 0.6831 (mt0) REVERT: D 69 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7182 (tm-30) REVERT: D 566 ASN cc_start: 0.8057 (t0) cc_final: 0.7848 (t0) REVERT: D 605 ASP cc_start: 0.7963 (m-30) cc_final: 0.7645 (m-30) REVERT: D 636 GLU cc_start: 0.7142 (pm20) cc_final: 0.6693 (pm20) REVERT: D 695 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7630 (m) REVERT: D 952 ASP cc_start: 0.7858 (m-30) cc_final: 0.7323 (m-30) REVERT: D 980 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7714 (ttmm) REVERT: D 982 TYR cc_start: 0.8362 (p90) cc_final: 0.7870 (p90) REVERT: D 1012 ASP cc_start: 0.8129 (m-30) cc_final: 0.7916 (m-30) REVERT: D 1124 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7443 (mp0) outliers start: 55 outliers final: 41 residues processed: 361 average time/residue: 0.1713 time to fit residues: 90.2104 Evaluate side-chains 381 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 335 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 627 ASN Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 706 ASP Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 199 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 GLN C 668 ASN D 204 GLN D 865 GLN D 976 GLN D1172 ASN ** D1181 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 = 0.3986 r_free = 0.3986 target = 0.157934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125083 restraints weight = 28299.298| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.46 r_work: 0.3419 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20196 Z= 0.142 Angle : 0.511 12.890 27414 Z= 0.277 Chirality : 0.040 0.168 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.703 85.578 2888 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.47 % Allowed : 15.15 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.06 (0.17), residues: 2376 helix: 2.10 (0.16), residues: 1078 sheet: 0.26 (0.32), residues: 275 loop : -2.47 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.013 0.001 TYR D 788 PHE 0.022 0.001 PHE D 684 TRP 0.025 0.001 TRP C 643 HIS 0.006 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (20196) covalent geometry : angle 0.51113 / 0.28 (27414) hydrogen bonds : bond 0.06011 / 6.01 ( 825) hydrogen bonds : angle 3.80876 / 3.41 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6362 (tm-30) REVERT: C 183 GLU cc_start: 0.6661 (pm20) cc_final: 0.6110 (pm20) REVERT: C 272 ASP cc_start: 0.6931 (p0) cc_final: 0.6626 (p0) REVERT: C 345 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 583 TYR cc_start: 0.6238 (t80) cc_final: 0.5769 (t80) REVERT: C 636 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 723 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7128 (tm-30) REVERT: C 733 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: C 861 LEU cc_start: 0.7732 (mt) cc_final: 0.7490 (mt) REVERT: C 943 SER cc_start: 0.7334 (t) cc_final: 0.7113 (t) REVERT: C 992 ASP cc_start: 0.7310 (t70) cc_final: 0.7040 (t70) REVERT: C 1001 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6897 (mtt90) REVERT: C 1063 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 1142 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8138 (mmtt) REVERT: D 50 GLN cc_start: 0.7136 (mt0) cc_final: 0.6815 (mt0) REVERT: D 69 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 275 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5297 (m-30) REVERT: D 566 ASN cc_start: 0.8105 (t0) cc_final: 0.7902 (t0) REVERT: D 605 ASP cc_start: 0.8023 (m-30) cc_final: 0.7729 (m-30) REVERT: D 636 GLU cc_start: 0.7223 (pm20) cc_final: 0.6840 (pm20) REVERT: D 695 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (m) REVERT: D 952 ASP cc_start: 0.7970 (m-30) cc_final: 0.7464 (m-30) REVERT: D 980 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7733 (ttmm) REVERT: D 982 TYR cc_start: 0.8380 (p90) cc_final: 0.7936 (p90) REVERT: D 997 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6654 (mm-30) REVERT: D 1012 ASP cc_start: 0.8166 (m-30) cc_final: 0.7947 (m-30) REVERT: D 1124 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7484 (mp0) outliers start: 52 outliers final: 38 residues processed: 362 average time/residue: 0.1703 time to fit residues: 89.7623 Evaluate side-chains 378 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 217 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 192 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 277 GLN C 522 ASN D 204 GLN D 865 GLN D 976 GLN ** D1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123875 restraints weight = 28202.803| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.44 r_work: 0.3410 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20196 Z= 0.168 Angle : 0.536 13.130 27414 Z= 0.289 Chirality : 0.040 0.169 3012 Planarity : 0.004 0.044 3474 Dihedral : 10.759 85.151 2888 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.66 % Allowed : 15.34 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.01 (0.17), residues: 2376 helix: 2.03 (0.16), residues: 1075 sheet: 0.25 (0.32), residues: 277 loop : -2.48 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.022 0.001 TYR D 615 PHE 0.021 0.001 PHE D 684 TRP 0.025 0.001 TRP C 643 HIS 0.007 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (20196) covalent geometry : angle 0.53642 / 0.29 (27414) hydrogen bonds : bond 0.06687 / 6.68 ( 825) hydrogen bonds : angle 3.91136 / 3.50 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6703 (pm20) cc_final: 0.6206 (pm20) REVERT: C 272 ASP cc_start: 0.6903 (p0) cc_final: 0.6583 (p0) REVERT: C 345 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 468 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7954 (t) REVERT: C 583 TYR cc_start: 0.6241 (t80) cc_final: 0.5777 (t80) REVERT: C 586 ARG cc_start: 0.7258 (mmm160) cc_final: 0.6884 (mmm-85) REVERT: C 636 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7320 (mt-10) REVERT: C 666 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8195 (mt) REVERT: C 723 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7148 (tm-30) REVERT: C 733 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: C 861 LEU cc_start: 0.7758 (mt) cc_final: 0.7543 (mt) REVERT: C 943 SER cc_start: 0.7380 (t) cc_final: 0.7173 (t) REVERT: C 1001 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6955 (mtt90) REVERT: C 1063 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 1142 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8164 (mmtt) REVERT: D 50 GLN cc_start: 0.7115 (mt0) cc_final: 0.6801 (mt0) REVERT: D 69 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 108 LEU cc_start: 0.8078 (tp) cc_final: 0.7812 (tp) REVERT: D 204 GLN cc_start: 0.7959 (mt0) cc_final: 0.7741 (mt0) REVERT: D 275 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.5458 (m-30) REVERT: D 566 ASN cc_start: 0.8125 (t0) cc_final: 0.7916 (t0) REVERT: D 605 ASP cc_start: 0.8015 (m-30) cc_final: 0.7720 (m-30) REVERT: D 636 GLU cc_start: 0.7209 (pm20) cc_final: 0.6867 (pm20) REVERT: D 952 ASP cc_start: 0.7990 (m-30) cc_final: 0.7476 (m-30) REVERT: D 980 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7758 (ttmm) REVERT: D 982 TYR cc_start: 0.8379 (p90) cc_final: 0.7933 (p90) REVERT: D 1012 ASP cc_start: 0.8177 (m-30) cc_final: 0.7953 (m-30) REVERT: D 1124 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7465 (mp0) outliers start: 56 outliers final: 45 residues processed: 367 average time/residue: 0.1650 time to fit residues: 87.6969 Evaluate side-chains 385 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 627 ASN Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 986 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 197 optimal weight: 0.0040 chunk 163 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 ASN D 865 GLN D 951 GLN D 976 GLN ** D1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124093 restraints weight = 27943.284| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.43 r_work: 0.3403 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20196 Z= 0.159 Angle : 0.536 13.430 27414 Z= 0.289 Chirality : 0.040 0.166 3012 Planarity : 0.004 0.044 3474 Dihedral : 10.756 84.930 2888 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.75 % Allowed : 15.43 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.03 (0.17), residues: 2376 helix: 2.01 (0.16), residues: 1076 sheet: 0.23 (0.31), residues: 277 loop : -2.50 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.020 0.001 TYR D 615 PHE 0.025 0.001 PHE D 684 TRP 0.026 0.001 TRP C 643 HIS 0.007 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (20196) covalent geometry : angle 0.53649 / 0.29 (27414) hydrogen bonds : bond 0.06553 / 6.54 ( 825) hydrogen bonds : angle 3.89827 / 3.48 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6730 (pm20) cc_final: 0.6273 (pm20) REVERT: C 272 ASP cc_start: 0.6904 (p0) cc_final: 0.6587 (p0) REVERT: C 345 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 468 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7942 (t) REVERT: C 583 TYR cc_start: 0.6237 (t80) cc_final: 0.5772 (t80) REVERT: C 586 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6867 (mmm-85) REVERT: C 636 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 666 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8178 (mt) REVERT: C 723 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7132 (tm-30) REVERT: C 733 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: C 861 LEU cc_start: 0.7757 (mt) cc_final: 0.7541 (mt) REVERT: C 943 SER cc_start: 0.7401 (t) cc_final: 0.7183 (t) REVERT: C 1001 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6828 (mtt90) REVERT: C 1063 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 1142 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8156 (mmtt) REVERT: D 50 GLN cc_start: 0.7128 (mt0) cc_final: 0.6805 (mt0) REVERT: D 69 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 275 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5344 (m-30) REVERT: D 566 ASN cc_start: 0.8132 (t0) cc_final: 0.7929 (t0) REVERT: D 605 ASP cc_start: 0.8008 (m-30) cc_final: 0.7711 (m-30) REVERT: D 636 GLU cc_start: 0.7218 (pm20) cc_final: 0.6886 (pm20) REVERT: D 695 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7623 (m) REVERT: D 952 ASP cc_start: 0.7988 (m-30) cc_final: 0.7475 (m-30) REVERT: D 980 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7759 (ttmm) REVERT: D 982 TYR cc_start: 0.8367 (p90) cc_final: 0.7884 (p90) REVERT: D 1012 ASP cc_start: 0.8180 (m-30) cc_final: 0.7945 (m-30) REVERT: D 1030 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6975 (ttp-110) REVERT: D 1124 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7443 (mp0) outliers start: 58 outliers final: 45 residues processed: 364 average time/residue: 0.1753 time to fit residues: 92.7745 Evaluate side-chains 388 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 986 GLN Chi-restraints excluded: chain D residue 1030 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 219 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 158 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 ASN D 204 GLN D 865 GLN D 976 GLN ** D1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124165 restraints weight = 28099.116| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.46 r_work: 0.3407 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20196 Z= 0.152 Angle : 0.536 13.589 27414 Z= 0.288 Chirality : 0.040 0.164 3012 Planarity : 0.004 0.044 3474 Dihedral : 10.755 84.680 2888 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.42 % Allowed : 15.91 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.01 (0.17), residues: 2376 helix: 2.03 (0.16), residues: 1074 sheet: 0.25 (0.31), residues: 277 loop : -2.50 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.019 0.001 TYR D 615 PHE 0.025 0.001 PHE D 684 TRP 0.026 0.001 TRP C 643 HIS 0.006 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20196) covalent geometry : angle 0.53578 / 0.29 (27414) hydrogen bonds : bond 0.06395 / 6.39 ( 825) hydrogen bonds : angle 3.87026 / 3.45 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6350 (tm-30) REVERT: C 183 GLU cc_start: 0.6741 (pm20) cc_final: 0.6262 (pm20) REVERT: C 272 ASP cc_start: 0.6914 (p0) cc_final: 0.6624 (p0) REVERT: C 345 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 468 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.7949 (t) REVERT: C 583 TYR cc_start: 0.6234 (t80) cc_final: 0.5772 (t80) REVERT: C 586 ARG cc_start: 0.7225 (mmm160) cc_final: 0.6850 (mmm-85) REVERT: C 636 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7306 (mt-10) REVERT: C 666 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8165 (mt) REVERT: C 723 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7111 (tm-30) REVERT: C 733 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: C 861 LEU cc_start: 0.7744 (mt) cc_final: 0.7525 (mt) REVERT: C 943 SER cc_start: 0.7396 (t) cc_final: 0.7179 (t) REVERT: C 1001 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6836 (mtt90) REVERT: C 1063 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 1142 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8165 (mmtt) REVERT: D 50 GLN cc_start: 0.7132 (mt0) cc_final: 0.6806 (mt0) REVERT: D 69 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7282 (tm-30) REVERT: D 108 LEU cc_start: 0.8071 (tp) cc_final: 0.7780 (tp) REVERT: D 566 ASN cc_start: 0.8132 (t0) cc_final: 0.7925 (t0) REVERT: D 605 ASP cc_start: 0.7989 (m-30) cc_final: 0.7708 (m-30) REVERT: D 636 GLU cc_start: 0.7231 (pm20) cc_final: 0.6892 (pm20) REVERT: D 952 ASP cc_start: 0.7991 (m-30) cc_final: 0.7473 (m-30) REVERT: D 980 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7764 (ttmm) REVERT: D 982 TYR cc_start: 0.8353 (p90) cc_final: 0.7860 (p90) REVERT: D 1012 ASP cc_start: 0.8188 (m-30) cc_final: 0.7954 (m-30) REVERT: D 1030 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7007 (ttp-110) REVERT: D 1124 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7455 (mp0) outliers start: 51 outliers final: 43 residues processed: 363 average time/residue: 0.1798 time to fit residues: 94.8997 Evaluate side-chains 384 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 643 TRP Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 949 GLU Chi-restraints excluded: chain D residue 986 GLN Chi-restraints excluded: chain D residue 1030 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Chi-restraints excluded: chain D residue 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 220 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 111 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 ASN D 204 GLN D 865 GLN D 976 GLN ** D1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.157321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124484 restraints weight = 28273.224| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.44 r_work: 0.3415 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20196 Z= 0.143 Angle : 0.531 13.645 27414 Z= 0.286 Chirality : 0.040 0.162 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.743 84.518 2888 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.66 % Allowed : 15.67 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.02 (0.17), residues: 2376 helix: 2.07 (0.16), residues: 1074 sheet: 0.25 (0.31), residues: 277 loop : -2.49 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1025 TYR 0.018 0.001 TYR D 615 PHE 0.025 0.001 PHE D 624 TRP 0.026 0.001 TRP C 643 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (20196) covalent geometry : angle 0.53110 / 0.29 (27414) hydrogen bonds : bond 0.06185 / 6.19 ( 825) hydrogen bonds : angle 3.83503 / 3.42 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4873.62 seconds wall clock time: 84 minutes 12.81 seconds (5052.81 seconds total)