Starting phenix.real_space_refine on Thu Jan 23 08:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_44490.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_44490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_44490.map" model { file = "/net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_44490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf5_44490/01_2025/9bf5_44490.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.58, per 1000 atoms: 0.64 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: 4.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 7.02 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: 7.94 Time building geometry restraints manager: 5.27 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=" CA PHE D 970 " pdb=" CB PHE D 970 " ideal model delta sigma weight residual 1.528 1.562 -0.034 2.61e-02 1.47e+03 1.71e+00 bond pdb=" CB ASP D 359 " pdb=" CG ASP D 359 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.60e+00 bond pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB GLU D 284 " pdb=" CG GLU D 284 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C3' DT B 19 " pdb=" C2' DT B 19 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 20191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 27315 2.89 - 5.77: 97 5.77 - 8.66: 1 8.66 - 11.54: 0 11.54 - 14.43: 1 Bond angle restraints: 27414 Sorted by residual: 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=" CA GLU D 284 " pdb=" CB GLU D 284 " pdb=" CG GLU D 284 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" N VAL D1152 " pdb=" CA VAL D1152 " pdb=" C VAL D1152 " ideal model delta sigma weight residual 113.20 110.15 3.05 9.60e-01 1.09e+00 1.01e+01 angle pdb=" N GLU D 183 " pdb=" CA GLU D 183 " pdb=" C GLU D 183 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.68e+00 angle pdb=" CB GLU D 284 " pdb=" CG GLU D 284 " pdb=" CD GLU D 284 " ideal model delta sigma weight residual 112.60 117.80 -5.20 1.70e+00 3.46e-01 9.37e+00 ... (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: 1960 0.030 - 0.060: 723 0.060 - 0.090: 192 0.090 - 0.120: 120 0.120 - 0.150: 17 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: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.380 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.002 0.037 20196 Z= 0.146 Angle : 0.502 14.427 27414 Z= 0.281 Chirality : 0.038 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.001 TRP C 643 HIS 0.008 0.001 HIS C 836 PHE 0.027 0.001 PHE D 684 TYR 0.018 0.001 TYR D 413 ARG 0.008 0.000 ARG C 233 *********************** 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 : 2.232 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: 0.4069 time to fit residues: 197.4437 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 : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN C 817 ASN C 821 GLN C 938 HIS C1078 ASN D 204 GLN D 458 HIS D 566 ASN D 865 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126213 restraints weight = 28217.702| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.43 r_work: 0.3451 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0878 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= 0.183 Angle : 0.503 9.989 27414 Z= 0.273 Chirality : 0.039 0.165 3012 Planarity : 0.004 0.048 3474 Dihedral : 10.678 88.407 2888 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.90 % Allowed : 11.92 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2376 helix: 1.91 (0.16), residues: 1091 sheet: 0.09 (0.32), residues: 281 loop : -2.52 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 643 HIS 0.007 0.001 HIS C 836 PHE 0.022 0.001 PHE D 684 TYR 0.017 0.001 TYR D 413 ARG 0.007 0.000 ARG C 233 *********************** 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 374 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6622 (tm-30) cc_final: 0.6271 (tm-30) REVERT: C 212 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8348 (ttm110) REVERT: C 272 ASP cc_start: 0.6991 (p0) cc_final: 0.6576 (p0) REVERT: C 323 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5623 (mt-10) REVERT: C 327 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 345 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7140 (tm-30) REVERT: C 469 TYR cc_start: 0.8258 (m-10) cc_final: 0.8044 (m-10) REVERT: C 583 TYR cc_start: 0.6187 (t80) cc_final: 0.5700 (t80) REVERT: C 636 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 861 LEU cc_start: 0.7719 (mt) cc_final: 0.7454 (mt) REVERT: C 992 ASP cc_start: 0.7302 (t70) cc_final: 0.7038 (t70) REVERT: C 1142 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8099 (mmtt) REVERT: D 50 GLN cc_start: 0.7176 (mt0) cc_final: 0.6841 (mt0) REVERT: D 69 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 275 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.5069 (m-30) REVERT: D 289 GLN cc_start: 0.7758 (mm110) cc_final: 0.7538 (mm-40) REVERT: D 561 ASN cc_start: 0.8447 (t0) cc_final: 0.8246 (t0) REVERT: D 566 ASN cc_start: 0.8020 (t0) cc_final: 0.7794 (t0) REVERT: D 605 ASP cc_start: 0.7922 (m-30) cc_final: 0.7617 (m-30) REVERT: D 952 ASP cc_start: 0.7857 (m-30) cc_final: 0.7319 (m-30) REVERT: D 970 PHE cc_start: 0.7701 (m-10) cc_final: 0.7292 (m-80) REVERT: D 980 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7674 (ttmm) REVERT: D 982 TYR cc_start: 0.8377 (p90) cc_final: 0.7959 (p90) REVERT: D 1012 ASP cc_start: 0.8126 (m-30) cc_final: 0.7898 (m-30) REVERT: D 1059 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7001 (mt-10) REVERT: D 1085 ASP cc_start: 0.7275 (t0) cc_final: 0.6360 (t0) REVERT: D 1124 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 40 outliers final: 25 residues processed: 354 average time/residue: 0.3987 time to fit residues: 204.1274 Evaluate side-chains 357 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 329 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG 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 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 938 HIS Chi-restraints excluded: chain C residue 957 LEU 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 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 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 108 optimal weight: 0.7980 chunk 224 optimal weight: 0.0670 chunk 25 optimal weight: 0.3980 chunk 206 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 185 optimal weight: 0.0980 chunk 198 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 668 ASN C1078 ASN C1176 ASN D 204 GLN D 865 GLN D 951 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127355 restraints weight = 28165.086| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.44 r_work: 0.3467 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20196 Z= 0.150 Angle : 0.472 10.417 27414 Z= 0.256 Chirality : 0.038 0.162 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.565 88.273 2888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.09 % Allowed : 12.49 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2376 helix: 2.11 (0.16), residues: 1085 sheet: 0.17 (0.31), residues: 289 loop : -2.47 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 643 HIS 0.008 0.001 HIS C 938 PHE 0.023 0.001 PHE D 684 TYR 0.013 0.001 TYR D 413 ARG 0.009 0.000 ARG C 233 *********************** 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 370 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 2.243 Fit side-chains REVERT: C 69 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6252 (tm-30) REVERT: C 212 ARG cc_start: 0.8555 (ttm170) cc_final: 0.8346 (ttm110) REVERT: C 272 ASP cc_start: 0.6981 (p0) cc_final: 0.6605 (p0) REVERT: C 345 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 583 TYR cc_start: 0.6169 (t80) cc_final: 0.5702 (t80) REVERT: C 636 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7357 (mt-10) REVERT: C 723 GLU cc_start: 0.7569 (tp30) cc_final: 0.7248 (tm-30) REVERT: C 861 LEU cc_start: 0.7698 (mt) cc_final: 0.7447 (mt) REVERT: C 992 ASP cc_start: 0.7323 (t70) cc_final: 0.7026 (t70) REVERT: C 1063 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 1142 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8105 (mmtt) REVERT: C 1177 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7726 (mpt180) REVERT: D 50 GLN cc_start: 0.7170 (mt0) cc_final: 0.6832 (mt0) REVERT: D 69 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 275 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.5136 (m-30) REVERT: D 289 GLN cc_start: 0.7731 (mm110) cc_final: 0.7499 (mm-40) REVERT: D 561 ASN cc_start: 0.8538 (t0) cc_final: 0.8329 (t0) REVERT: D 566 ASN cc_start: 0.8071 (t0) cc_final: 0.7828 (t0) REVERT: D 601 LEU cc_start: 0.8512 (mp) cc_final: 0.8291 (mt) REVERT: D 605 ASP cc_start: 0.7945 (m-30) cc_final: 0.7665 (m-30) REVERT: D 636 GLU cc_start: 0.7097 (pm20) cc_final: 0.6501 (pm20) REVERT: D 695 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 952 ASP cc_start: 0.7835 (m-30) cc_final: 0.7311 (m-30) REVERT: D 970 PHE cc_start: 0.7689 (m-10) cc_final: 0.7281 (m-80) REVERT: D 980 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7679 (ttmm) REVERT: D 982 TYR cc_start: 0.8377 (p90) cc_final: 0.7899 (p90) REVERT: D 997 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6780 (mm-30) REVERT: D 1012 ASP cc_start: 0.8113 (m-30) cc_final: 0.7888 (m-30) REVERT: D 1124 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7440 (mp0) outliers start: 44 outliers final: 28 residues processed: 346 average time/residue: 0.4010 time to fit residues: 200.3980 Evaluate side-chains 353 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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 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 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 957 LEU 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 214 LEU Chi-restraints excluded: chain D residue 261 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 949 GLU Chi-restraints excluded: chain D residue 1124 GLU Chi-restraints excluded: chain D residue 1164 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 211 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 215 optimal weight: 0.0870 chunk 201 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 817 ASN C 821 GLN D 204 GLN D 865 GLN D 976 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126829 restraints weight = 28432.633| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.44 r_work: 0.3457 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20196 Z= 0.158 Angle : 0.470 11.098 27414 Z= 0.254 Chirality : 0.038 0.163 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.511 87.876 2888 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.09 % Allowed : 13.53 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2376 helix: 2.18 (0.16), residues: 1085 sheet: 0.31 (0.32), residues: 275 loop : -2.41 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 643 HIS 0.005 0.001 HIS C 836 PHE 0.023 0.001 PHE D 684 TYR 0.011 0.001 TYR D 615 ARG 0.009 0.000 ARG C 233 *********************** 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 374 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6322 (tm-30) REVERT: C 183 GLU cc_start: 0.6538 (pm20) cc_final: 0.5947 (pm20) REVERT: C 191 GLN cc_start: 0.7198 (mt0) cc_final: 0.6498 (mm110) REVERT: C 212 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8358 (ttm110) REVERT: C 272 ASP cc_start: 0.6920 (p0) cc_final: 0.6590 (p0) REVERT: C 636 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 723 GLU cc_start: 0.7549 (tp30) cc_final: 0.7250 (tm-30) REVERT: C 817 ASN cc_start: 0.8247 (t0) cc_final: 0.7877 (t0) REVERT: C 861 LEU cc_start: 0.7708 (mt) cc_final: 0.7473 (mt) REVERT: C 992 ASP cc_start: 0.7315 (t70) cc_final: 0.7044 (t70) REVERT: C 1063 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 1142 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8086 (mmtt) REVERT: C 1177 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7416 (mpt180) REVERT: D 50 GLN cc_start: 0.7149 (mt0) cc_final: 0.6824 (mt0) REVERT: D 69 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7253 (tm-30) REVERT: D 275 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5144 (m-30) REVERT: D 289 GLN cc_start: 0.7725 (mm110) cc_final: 0.7499 (mm-40) REVERT: D 566 ASN cc_start: 0.8093 (t0) cc_final: 0.7892 (t0) REVERT: D 601 LEU cc_start: 0.8532 (mp) cc_final: 0.8318 (mt) REVERT: D 605 ASP cc_start: 0.7958 (m-30) cc_final: 0.7676 (m-30) REVERT: D 636 GLU cc_start: 0.7114 (pm20) cc_final: 0.6592 (pm20) REVERT: D 695 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7541 (m) REVERT: D 952 ASP cc_start: 0.7876 (m-30) cc_final: 0.7360 (m-30) REVERT: D 970 PHE cc_start: 0.7696 (m-10) cc_final: 0.7305 (m-80) REVERT: D 980 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7711 (ttmm) REVERT: D 982 TYR cc_start: 0.8366 (p90) cc_final: 0.7874 (p90) REVERT: D 997 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6762 (mm-30) REVERT: D 1012 ASP cc_start: 0.8105 (m-30) cc_final: 0.7888 (m-30) REVERT: D 1124 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7473 (mp0) outliers start: 44 outliers final: 33 residues processed: 349 average time/residue: 0.4026 time to fit residues: 203.0475 Evaluate side-chains 358 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 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 821 GLN 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 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 421 ARG Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 584 HIS Chi-restraints excluded: chain D residue 630 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 224 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 HIS C 668 ASN C1176 ASN D 204 GLN D 865 GLN D 976 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124789 restraints weight = 28426.393| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.44 r_work: 0.3427 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1300 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= 0.222 Angle : 0.503 12.224 27414 Z= 0.270 Chirality : 0.039 0.168 3012 Planarity : 0.003 0.044 3474 Dihedral : 10.591 87.279 2888 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.42 % Allowed : 14.06 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2376 helix: 2.11 (0.16), residues: 1084 sheet: 0.27 (0.32), residues: 275 loop : -2.42 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 643 HIS 0.006 0.001 HIS C 836 PHE 0.023 0.001 PHE D 684 TYR 0.014 0.001 TYR D 788 ARG 0.009 0.000 ARG C 233 *********************** 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 378 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 2.303 Fit side-chains REVERT: C 183 GLU cc_start: 0.6578 (pm20) cc_final: 0.6036 (pm20) REVERT: C 212 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8362 (ttm110) REVERT: C 272 ASP cc_start: 0.6904 (p0) cc_final: 0.6572 (p0) REVERT: C 636 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 817 ASN cc_start: 0.8276 (t0) cc_final: 0.7862 (t0) REVERT: C 861 LEU cc_start: 0.7722 (mt) cc_final: 0.7488 (mt) REVERT: C 992 ASP cc_start: 0.7315 (t70) cc_final: 0.7038 (t70) REVERT: C 1001 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6893 (mtt90) REVERT: C 1063 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 1142 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8112 (mmtt) REVERT: C 1177 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7697 (mpt180) REVERT: D 35 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6859 (tp30) REVERT: D 50 GLN cc_start: 0.7188 (mt0) cc_final: 0.6829 (mt0) REVERT: D 69 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7224 (tm-30) REVERT: D 204 GLN cc_start: 0.8020 (mt0) cc_final: 0.7801 (mt0) REVERT: D 275 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.5366 (m-30) REVERT: D 284 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 289 GLN cc_start: 0.7764 (mm110) cc_final: 0.7541 (mm-40) REVERT: D 601 LEU cc_start: 0.8518 (mp) cc_final: 0.8301 (mt) REVERT: D 605 ASP cc_start: 0.7987 (m-30) cc_final: 0.7705 (m-30) REVERT: D 636 GLU cc_start: 0.7205 (pm20) cc_final: 0.6681 (pm20) REVERT: D 952 ASP cc_start: 0.7908 (m-30) cc_final: 0.7382 (m-30) REVERT: D 980 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7759 (ttmm) REVERT: D 982 TYR cc_start: 0.8373 (p90) cc_final: 0.7841 (p90) REVERT: D 1012 ASP cc_start: 0.8113 (m-30) cc_final: 0.7896 (m-30) REVERT: D 1124 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7475 (mp0) outliers start: 51 outliers final: 41 residues processed: 350 average time/residue: 0.3896 time to fit residues: 198.2981 Evaluate side-chains 371 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET 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 330 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 667 LEU 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 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 510 THR Chi-restraints excluded: chain D residue 551 VAL 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 706 ASP 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 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 134 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 85 optimal weight: 0.0170 chunk 148 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C1176 ASN D 566 ASN D 865 GLN D 976 GLN D1172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.157411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124426 restraints weight = 28171.278| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.45 r_work: 0.3409 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1411 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= 0.232 Angle : 0.519 12.974 27414 Z= 0.279 Chirality : 0.040 0.168 3012 Planarity : 0.004 0.045 3474 Dihedral : 10.662 86.610 2888 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.61 % Allowed : 14.34 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2376 helix: 2.07 (0.16), residues: 1078 sheet: 0.25 (0.32), residues: 275 loop : -2.45 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 643 HIS 0.006 0.001 HIS C 836 PHE 0.023 0.001 PHE D 684 TYR 0.014 0.001 TYR D 788 ARG 0.007 0.000 ARG C 233 *********************** 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 390 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 2.102 Fit side-chains REVERT: C 183 GLU cc_start: 0.6701 (pm20) cc_final: 0.6259 (pm20) REVERT: C 191 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6820 (mm110) REVERT: C 272 ASP cc_start: 0.6887 (p0) cc_final: 0.6579 (p0) REVERT: C 586 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6856 (mmm-85) REVERT: C 636 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 723 GLU cc_start: 0.7494 (tp30) cc_final: 0.7214 (tm-30) REVERT: C 733 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: C 817 ASN cc_start: 0.8299 (t0) cc_final: 0.7949 (t0) REVERT: C 861 LEU cc_start: 0.7755 (mt) cc_final: 0.7525 (mt) REVERT: C 1001 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6846 (mtt90) REVERT: C 1063 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 1142 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8176 (mmtt) REVERT: C 1177 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7733 (mpt180) REVERT: D 35 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6925 (tp30) REVERT: D 50 GLN cc_start: 0.7131 (mt0) cc_final: 0.6814 (mt0) REVERT: D 69 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 204 GLN cc_start: 0.8080 (mt0) cc_final: 0.7873 (mt0) REVERT: D 275 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5370 (m-30) REVERT: D 605 ASP cc_start: 0.8002 (m-30) cc_final: 0.7695 (m-30) REVERT: D 636 GLU cc_start: 0.7205 (pm20) cc_final: 0.6774 (pm20) REVERT: D 952 ASP cc_start: 0.8000 (m-30) cc_final: 0.7486 (m-30) REVERT: D 980 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7755 (ttmm) REVERT: D 982 TYR cc_start: 0.8396 (p90) cc_final: 0.7866 (p90) REVERT: D 1012 ASP cc_start: 0.8179 (m-30) cc_final: 0.7959 (m-30) REVERT: D 1124 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 55 outliers final: 43 residues processed: 364 average time/residue: 0.4015 time to fit residues: 213.5483 Evaluate side-chains 381 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 330 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 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 957 LEU 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 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 261 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 551 VAL 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 289 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 = 0.3948 r_free = 0.3948 target = 0.154805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121751 restraints weight = 28090.756| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.43 r_work: 0.3376 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20196 Z= 0.342 Angle : 0.581 13.129 27414 Z= 0.312 Chirality : 0.043 0.177 3012 Planarity : 0.004 0.049 3474 Dihedral : 10.799 85.769 2888 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.74 % Favored : 92.21 % Rotamer: Outliers : 2.66 % Allowed : 15.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2376 helix: 1.91 (0.16), residues: 1068 sheet: 0.19 (0.31), residues: 276 loop : -2.48 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 643 HIS 0.009 0.001 HIS C 836 PHE 0.022 0.002 PHE D 684 TYR 0.020 0.002 TYR D 788 ARG 0.010 0.000 ARG C 233 *********************** 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 391 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6669 (pm20) cc_final: 0.6074 (pm20) REVERT: C 184 VAL cc_start: 0.7907 (t) cc_final: 0.7661 (m) REVERT: C 272 ASP cc_start: 0.6888 (p0) cc_final: 0.6592 (p0) REVERT: C 345 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 468 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7973 (t) REVERT: C 636 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7274 (mt-10) REVERT: C 723 GLU cc_start: 0.7527 (tp30) cc_final: 0.7279 (tm-30) REVERT: C 733 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: C 817 ASN cc_start: 0.8331 (t0) cc_final: 0.7992 (t0) REVERT: C 861 LEU cc_start: 0.7794 (mt) cc_final: 0.7561 (mt) REVERT: C 1001 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7004 (mtt90) REVERT: C 1011 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7028 (mp0) REVERT: C 1063 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 1082 GLU cc_start: 0.6478 (tp30) cc_final: 0.6198 (tp30) REVERT: C 1142 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8204 (mmtt) REVERT: D 50 GLN cc_start: 0.7167 (mt0) cc_final: 0.6866 (mt0) REVERT: D 69 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7305 (tm-30) REVERT: D 204 GLN cc_start: 0.8156 (mt0) cc_final: 0.7952 (mt0) REVERT: D 275 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.5699 (m-30) REVERT: D 319 GLU cc_start: 0.7546 (tp30) cc_final: 0.7219 (tp30) REVERT: D 408 GLU cc_start: 0.7259 (mp0) cc_final: 0.6935 (mt-10) REVERT: D 605 ASP cc_start: 0.8048 (m-30) cc_final: 0.7738 (m-30) REVERT: D 636 GLU cc_start: 0.7265 (pm20) cc_final: 0.6870 (pm20) REVERT: D 952 ASP cc_start: 0.8030 (m-30) cc_final: 0.7469 (m-30) REVERT: D 980 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7792 (ttmm) REVERT: D 982 TYR cc_start: 0.8403 (p90) cc_final: 0.7926 (p90) REVERT: D 1012 ASP cc_start: 0.8200 (m-30) cc_final: 0.7962 (m-30) REVERT: D 1030 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7000 (ttp-110) REVERT: D 1124 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7533 (mp0) outliers start: 56 outliers final: 40 residues processed: 367 average time/residue: 0.3905 time to fit residues: 207.8817 Evaluate side-chains 379 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET 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 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 374 LEU 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 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 957 LEU 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 261 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 551 VAL 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 160 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN C 522 ASN D 189 ASN D 277 GLN D 566 ASN D 865 GLN D 976 GLN ** D1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122410 restraints weight = 28333.452| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.44 r_work: 0.3381 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20196 Z= 0.301 Angle : 0.575 14.041 27414 Z= 0.307 Chirality : 0.042 0.168 3012 Planarity : 0.004 0.047 3474 Dihedral : 10.825 85.604 2888 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.80 % Allowed : 15.24 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2376 helix: 1.89 (0.16), residues: 1067 sheet: 0.15 (0.32), residues: 277 loop : -2.49 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 643 HIS 0.008 0.001 HIS C 836 PHE 0.024 0.002 PHE D 684 TYR 0.019 0.002 TYR D 615 ARG 0.009 0.000 ARG C 233 *********************** 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 394 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 335 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6688 (pm20) cc_final: 0.6122 (pm20) REVERT: C 272 ASP cc_start: 0.6907 (p0) cc_final: 0.6606 (p0) REVERT: C 345 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 468 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7982 (t) REVERT: C 586 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6935 (mmm-85) REVERT: C 636 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 723 GLU cc_start: 0.7510 (tp30) cc_final: 0.7281 (tm-30) REVERT: C 733 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: C 817 ASN cc_start: 0.8301 (t0) cc_final: 0.7957 (t0) REVERT: C 861 LEU cc_start: 0.7781 (mt) cc_final: 0.7524 (mt) REVERT: C 1001 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6981 (mtt90) REVERT: C 1011 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7038 (mp0) REVERT: C 1063 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 1082 GLU cc_start: 0.6418 (tp30) cc_final: 0.6181 (tp30) REVERT: C 1142 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8208 (mmtt) REVERT: D 50 GLN cc_start: 0.7170 (mt0) cc_final: 0.6864 (mt0) REVERT: D 69 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 275 ASP cc_start: 0.6529 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: D 319 GLU cc_start: 0.7547 (tp30) cc_final: 0.7216 (tp30) REVERT: D 605 ASP cc_start: 0.8031 (m-30) cc_final: 0.7716 (m-30) REVERT: D 636 GLU cc_start: 0.7251 (pm20) cc_final: 0.6867 (pm20) REVERT: D 753 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5752 (tp30) REVERT: D 952 ASP cc_start: 0.8023 (m-30) cc_final: 0.7462 (m-30) REVERT: D 980 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7793 (ttmm) REVERT: D 982 TYR cc_start: 0.8404 (p90) cc_final: 0.7879 (p90) REVERT: D 1012 ASP cc_start: 0.8221 (m-30) cc_final: 0.7977 (m-30) REVERT: D 1030 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6968 (ttp-110) REVERT: D 1124 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7520 (mp0) outliers start: 59 outliers final: 45 residues processed: 370 average time/residue: 0.3895 time to fit residues: 211.2115 Evaluate side-chains 388 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 336 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET 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 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 447 THR 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 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1001 ARG 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 D residue 1 MET Chi-restraints excluded: chain D residue 3 VAL 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 261 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 458 HIS Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 551 VAL 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 753 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 173 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 46 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN C 522 ASN 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 = 0.3962 r_free = 0.3962 target = 0.155907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123105 restraints weight = 28022.082| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.41 r_work: 0.3387 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20196 Z= 0.264 Angle : 0.559 14.168 27414 Z= 0.299 Chirality : 0.041 0.168 3012 Planarity : 0.004 0.048 3474 Dihedral : 10.824 85.454 2888 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.52 % Allowed : 15.72 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2376 helix: 1.87 (0.16), residues: 1078 sheet: 0.16 (0.32), residues: 277 loop : -2.54 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 643 HIS 0.007 0.001 HIS C 836 PHE 0.024 0.001 PHE D 684 TYR 0.018 0.001 TYR D 615 ARG 0.009 0.000 ARG C 233 *********************** 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 389 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.6689 (pm20) cc_final: 0.6130 (pm20) REVERT: C 191 GLN cc_start: 0.7346 (mt0) cc_final: 0.6715 (mm110) REVERT: C 272 ASP cc_start: 0.6890 (p0) cc_final: 0.6592 (p0) REVERT: C 345 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 468 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7987 (t) REVERT: C 586 ARG cc_start: 0.7313 (mmm160) cc_final: 0.6951 (mmm-85) REVERT: C 636 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 723 GLU cc_start: 0.7491 (tp30) cc_final: 0.7277 (tm-30) REVERT: C 733 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: C 817 ASN cc_start: 0.8286 (t0) cc_final: 0.7936 (t0) REVERT: C 861 LEU cc_start: 0.7779 (mt) cc_final: 0.7547 (mt) REVERT: C 1001 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6537 (mpp-170) REVERT: C 1011 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7033 (mp0) REVERT: C 1063 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7362 (tm-30) REVERT: C 1142 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8250 (mmtt) REVERT: D 50 GLN cc_start: 0.7144 (mt0) cc_final: 0.6844 (mt0) REVERT: D 69 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7298 (tm-30) REVERT: D 108 LEU cc_start: 0.8048 (tp) cc_final: 0.7766 (tp) REVERT: D 275 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5467 (m-30) REVERT: D 319 GLU cc_start: 0.7536 (tp30) cc_final: 0.7206 (tp30) REVERT: D 605 ASP cc_start: 0.8009 (m-30) cc_final: 0.7700 (m-30) REVERT: D 636 GLU cc_start: 0.7260 (pm20) cc_final: 0.6868 (pm20) REVERT: D 753 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5758 (tp30) REVERT: D 952 ASP cc_start: 0.8011 (m-30) cc_final: 0.7500 (m-30) REVERT: D 980 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7801 (ttmm) REVERT: D 982 TYR cc_start: 0.8371 (p90) cc_final: 0.7839 (p90) REVERT: D 1012 ASP cc_start: 0.8175 (m-30) cc_final: 0.7922 (m-30) REVERT: D 1030 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6975 (ttp-110) REVERT: D 1124 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7510 (mp0) outliers start: 53 outliers final: 44 residues processed: 366 average time/residue: 0.3946 time to fit residues: 209.8309 Evaluate side-chains 388 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 447 THR 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 733 TYR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1001 ARG 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 D residue 1 MET Chi-restraints excluded: chain D residue 3 VAL 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 261 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 458 HIS Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 551 VAL 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 753 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 136 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 22 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN C 522 ASN 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 = 0.3978 r_free = 0.3978 target = 0.157270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124514 restraints weight = 28017.267| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.44 r_work: 0.3414 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20196 Z= 0.205 Angle : 0.533 14.742 27414 Z= 0.285 Chirality : 0.040 0.163 3012 Planarity : 0.004 0.047 3474 Dihedral : 10.752 85.457 2888 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.23 % Allowed : 16.00 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2376 helix: 2.03 (0.16), residues: 1076 sheet: 0.20 (0.31), residues: 277 loop : -2.49 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 643 HIS 0.005 0.001 HIS C 836 PHE 0.024 0.001 PHE D 684 TYR 0.016 0.001 TYR D 615 ARG 0.009 0.000 ARG C 233 ********************** 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 385 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6281 (tm-30) REVERT: C 183 GLU cc_start: 0.6755 (pm20) cc_final: 0.6281 (pm20) REVERT: C 191 GLN cc_start: 0.7289 (mt0) cc_final: 0.6653 (mm110) REVERT: C 272 ASP cc_start: 0.6896 (p0) cc_final: 0.6606 (p0) REVERT: C 345 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 468 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7958 (t) REVERT: C 586 ARG cc_start: 0.7224 (mmm160) cc_final: 0.6842 (mmm-85) REVERT: C 636 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7296 (mt-10) REVERT: C 666 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8215 (mt) REVERT: C 681 PHE cc_start: 0.8249 (t80) cc_final: 0.8040 (t80) REVERT: C 723 GLU cc_start: 0.7460 (tp30) cc_final: 0.7238 (tm-30) REVERT: C 817 ASN cc_start: 0.8265 (t0) cc_final: 0.7912 (t0) REVERT: C 861 LEU cc_start: 0.7755 (mt) cc_final: 0.7525 (mt) REVERT: C 1001 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6800 (mtt90) REVERT: C 1011 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7025 (mp0) REVERT: C 1063 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7322 (tm-30) REVERT: C 1142 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8231 (mmtt) REVERT: D 50 GLN cc_start: 0.7130 (mt0) cc_final: 0.6852 (mt0) REVERT: D 69 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 275 ASP cc_start: 0.6168 (OUTLIER) cc_final: 0.5241 (m-30) REVERT: D 319 GLU cc_start: 0.7543 (tp30) cc_final: 0.7207 (tp30) REVERT: D 605 ASP cc_start: 0.7985 (m-30) cc_final: 0.7695 (m-30) REVERT: D 636 GLU cc_start: 0.7210 (pm20) cc_final: 0.6805 (pm20) REVERT: D 695 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7633 (m) REVERT: D 753 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5758 (tp30) REVERT: D 952 ASP cc_start: 0.7994 (m-30) cc_final: 0.7479 (m-30) REVERT: D 980 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7774 (ttmm) REVERT: D 982 TYR cc_start: 0.8339 (p90) cc_final: 0.7812 (p90) REVERT: D 1012 ASP cc_start: 0.8174 (m-30) cc_final: 0.7930 (m-30) REVERT: D 1030 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6963 (ttp-110) REVERT: D 1124 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7501 (mp0) outliers start: 47 outliers final: 37 residues processed: 365 average time/residue: 0.3928 time to fit residues: 207.5288 Evaluate side-chains 378 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 447 THR 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 625 ILE Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1001 ARG 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 3 VAL 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 261 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 458 HIS Chi-restraints excluded: chain D residue 551 VAL 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 753 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 156 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 149 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN C 507 ASN C 522 ASN C 668 ASN D 865 GLN D 976 GLN ** 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 = 0.3989 r_free = 0.3989 target = 0.158168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125348 restraints weight = 28309.393| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.46 r_work: 0.3425 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1630 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= 0.189 Angle : 0.526 14.615 27414 Z= 0.281 Chirality : 0.039 0.162 3012 Planarity : 0.004 0.046 3474 Dihedral : 10.711 85.180 2888 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.28 % Allowed : 16.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2376 helix: 2.10 (0.16), residues: 1081 sheet: 0.26 (0.32), residues: 275 loop : -2.47 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 643 HIS 0.005 0.001 HIS C 836 PHE 0.024 0.001 PHE D 684 TYR 0.014 0.001 TYR D 615 ARG 0.008 0.000 ARG C 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9040.73 seconds wall clock time: 161 minutes 30.37 seconds (9690.37 seconds total)