Starting phenix.real_space_refine on Fri Aug 7 07:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.map" model { file = "/net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wxi_66347/08_2026/9wxi_66347.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 65 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 12070 2.51 5 N 3429 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 819 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 19, 'rna3p': 19} Chain: "B" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3796 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 4 Chain: "C" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4912 Classifications: {'peptide': 626} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 586} Chain: "D" Number of atoms: 9433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9433 Classifications: {'peptide': 1194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1133} Chain breaks: 2 Chain: "E" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 511 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 18} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11996 SG CYS D 338 55.203 84.720 84.184 1.00 74.35 S ATOM 12039 SG CYS D 344 56.997 85.542 87.392 1.00 73.55 S ATOM 12089 SG CYS D 351 55.074 88.128 85.328 1.00 64.39 S ATOM 12108 SG CYS D 354 53.125 85.573 86.816 1.00 68.52 S Time building chain proxies: 3.48, per 1000 atoms: 0.18 Number of scatterers: 19532 At special positions: 0 Unit cell: (111.552, 118.524, 178.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 62 16.00 P 65 15.00 Mg 1 11.99 O 3904 8.00 N 3429 7.00 C 12070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 741.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 351 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 354 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 338 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 344 " Number of angles added : 6 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 39 sheets defined 34.9% alpha, 22.8% beta 20 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'B' and resid 21 through 43 removed outlier: 3.636A pdb=" N MET B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 152 through 156 removed outlier: 4.046A pdb=" N TYR B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 189 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 241 through 254 Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 299 through 327 removed outlier: 4.313A pdb=" N GLU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 355 through 373 removed outlier: 4.642A pdb=" N TRP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.997A pdb=" N LYS B 426 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 489 through 499 removed outlier: 3.591A pdb=" N ILE B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 527 through 542 Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'C' and resid 43 through 66 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.514A pdb=" N SER C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 410 through 426 Processing helix chain 'C' and resid 459 through 462 removed outlier: 3.967A pdb=" N GLY C 462 " --> pdb=" O PRO C 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 462' Processing helix chain 'C' and resid 486 through 503 Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 554 through 569 removed outlier: 3.503A pdb=" N ALA C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 580 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 314 through 333 Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 423 through 443 Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 466 through 470 removed outlier: 3.564A pdb=" N VAL D 469 " --> pdb=" O ASN D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.556A pdb=" N SER D 505 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 610 through 626 Processing helix chain 'D' and resid 643 through 647 Processing helix chain 'D' and resid 669 through 673 removed outlier: 3.544A pdb=" N ALA D 673 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 691 removed outlier: 3.545A pdb=" N ASN D 691 " --> pdb=" O ASP D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 756 No H-bonds generated for 'chain 'D' and resid 754 through 756' Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 779 through 797 removed outlier: 3.728A pdb=" N GLN D 797 " --> pdb=" O ARG D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 805 through 809 Processing helix chain 'D' and resid 866 through 871 Processing helix chain 'D' and resid 872 through 876 Processing helix chain 'D' and resid 886 through 892 Processing helix chain 'D' and resid 922 through 928 removed outlier: 3.680A pdb=" N ILE D 927 " --> pdb=" O PRO D 923 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 928 " --> pdb=" O ASP D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 removed outlier: 3.624A pdb=" N LEU D 932 " --> pdb=" O ARG D 928 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN D 933 " --> pdb=" O GLN D 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 928 through 933' Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 1021 through 1024 Processing helix chain 'D' and resid 1048 through 1059 Processing helix chain 'D' and resid 1071 through 1075 Processing helix chain 'D' and resid 1090 through 1097 Processing helix chain 'D' and resid 1139 through 1149 Processing helix chain 'D' and resid 1152 through 1164 removed outlier: 3.591A pdb=" N ASP D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1168 Processing helix chain 'D' and resid 1186 through 1195 removed outlier: 4.133A pdb=" N PHE D1190 " --> pdb=" O ASN D1186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 117 through 120 removed outlier: 5.611A pdb=" N THR B 117 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 128 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 157 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'B' and resid 212 through 215 removed outlier: 4.601A pdb=" N ASP B 212 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 228 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 214 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 226 " --> pdb=" O ARG B 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.255A pdb=" N ILE B 350 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP B 344 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 348 " --> pdb=" O TRP B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 333 Processing sheet with id=AA6, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.270A pdb=" N LYS C 13 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 188 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB1, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB2, first strand: chain 'C' and resid 285 through 286 removed outlier: 5.225A pdb=" N THR C 437 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 237 through 239 removed outlier: 6.655A pdb=" N PHE C 238 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 392 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER C 365 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 297 through 298 Processing sheet with id=AB5, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB6, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 375 removed outlier: 3.635A pdb=" N ARG C 380 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 506 through 512 removed outlier: 6.963A pdb=" N VAL C 547 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 511 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 545 " --> pdb=" O TYR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 515 through 518 Processing sheet with id=AC1, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.522A pdb=" N VAL D 115 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG D 166 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.522A pdb=" N VAL D 115 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG D 166 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR D 22 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN D 215 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU D 24 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE D 213 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 32 through 42 removed outlier: 5.125A pdb=" N GLU D 35 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 20.336A pdb=" N ARG D 48 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 16.498A pdb=" N LEU D 155 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLN D 50 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N TYR D 157 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN D 52 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU D 159 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 54 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR D 154 " --> pdb=" O THR D 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 312 through 313 Processing sheet with id=AC5, first strand: chain 'D' and resid 312 through 313 removed outlier: 3.546A pdb=" N GLY D 273 " --> pdb=" O THR D 465 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 281 through 282 removed outlier: 6.353A pdb=" N HIS D 301 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N PHE D 406 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 281 through 282 removed outlier: 6.005A pdb=" N ALA D 399 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 518 through 519 Processing sheet with id=AC9, first strand: chain 'D' and resid 523 through 526 Processing sheet with id=AD1, first strand: chain 'D' and resid 537 through 538 removed outlier: 3.549A pdb=" N LEU D 537 " --> pdb=" O ILE D 885 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 914 through 916 removed outlier: 5.611A pdb=" N HIS D 565 " --> pdb=" O ASN D1045 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 914 through 916 removed outlier: 5.611A pdb=" N HIS D 565 " --> pdb=" O ASN D1045 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 582 through 585 removed outlier: 4.302A pdb=" N GLY D 584 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS D 596 " --> pdb=" O ARG D1027 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 602 through 603 Processing sheet with id=AD6, first strand: chain 'D' and resid 639 through 641 Processing sheet with id=AD7, first strand: chain 'D' and resid 776 through 777 removed outlier: 7.159A pdb=" N ILE D 651 " --> pdb=" O MET D 666 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 650 " --> pdb=" O PHE D 843 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 674 through 676 Processing sheet with id=AD9, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.683A pdb=" N TYR D 825 " --> pdb=" O LEU D 832 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 830 " --> pdb=" O LYS D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 893 through 895 Processing sheet with id=AE3, first strand: chain 'D' and resid 955 through 957 777 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3894 1.33 - 1.45: 6024 1.45 - 1.57: 9939 1.57 - 1.70: 141 1.70 - 1.82: 95 Bond restraints: 20093 Sorted by residual: bond pdb=" N3B ANP B 602 " pdb=" PG ANP B 602 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sigma weight residual 1.700 1.605 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" CG LEU D1024 " pdb=" CD2 LEU D1024 " ideal model delta sigma weight residual 1.521 1.651 -0.130 3.30e-02 9.18e+02 1.55e+01 bond pdb=" NE ARG D 915 " pdb=" CZ ARG D 915 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" CA SER C 240 " pdb=" CB SER C 240 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.53e-02 4.27e+03 1.11e+01 ... (remaining 20088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 25284 2.95 - 5.89: 1887 5.89 - 8.84: 284 8.84 - 11.79: 35 11.79 - 14.74: 3 Bond angle restraints: 27493 Sorted by residual: angle pdb=" CA ASP D 687 " pdb=" CB ASP D 687 " pdb=" CG ASP D 687 " ideal model delta sigma weight residual 112.60 120.05 -7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" O3' U A 10 " pdb=" P G A 11 " pdb=" O5' G A 11 " ideal model delta sigma weight residual 104.00 117.93 -13.93 1.90e+00 2.77e-01 5.38e+01 angle pdb=" CA ASP C 458 " pdb=" CB ASP C 458 " pdb=" CG ASP C 458 " ideal model delta sigma weight residual 112.60 119.85 -7.25 1.00e+00 1.00e+00 5.26e+01 angle pdb=" CA ASP B 149 " pdb=" CB ASP B 149 " pdb=" CG ASP B 149 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" CA ASP D 152 " pdb=" CB ASP D 152 " pdb=" CG ASP D 152 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.44e+01 ... (remaining 27488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 11706 35.82 - 71.64: 428 71.64 - 107.46: 64 107.46 - 143.28: 1 143.28 - 179.10: 2 Dihedral angle restraints: 12201 sinusoidal: 5618 harmonic: 6583 Sorted by residual: dihedral pdb=" O4' U E 15 " pdb=" C1' U E 15 " pdb=" N1 U E 15 " pdb=" C2 U E 15 " ideal model delta sinusoidal sigma weight residual -128.00 51.10 -179.10 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASN D 672 " pdb=" C ASN D 672 " pdb=" N ALA D 673 " pdb=" CA ALA D 673 " ideal model delta harmonic sigma weight residual 180.00 144.91 35.09 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CA ILE B 421 " pdb=" C ILE B 421 " pdb=" N GLU B 422 " pdb=" CA GLU B 422 " ideal model delta harmonic sigma weight residual -180.00 -147.60 -32.40 0 5.00e+00 4.00e-02 4.20e+01 ... (remaining 12198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2374 0.105 - 0.209: 570 0.209 - 0.314: 61 0.314 - 0.418: 6 0.418 - 0.523: 2 Chirality restraints: 3013 Sorted by residual: chirality pdb=" P C E 2 " pdb=" OP1 C E 2 " pdb=" OP2 C E 2 " pdb=" O5' C E 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" P G A 11 " pdb=" OP1 G A 11 " pdb=" OP2 G A 11 " pdb=" O5' G A 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA HIS D 392 " pdb=" N HIS D 392 " pdb=" C HIS D 392 " pdb=" CB HIS D 392 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 3010 not shown) Planarity restraints: 3354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 5 " 0.064 2.00e-02 2.50e+03 2.75e-02 2.08e+01 pdb=" N9 A A 5 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A A 5 " -0.018 2.00e-02 2.50e+03 pdb=" N7 A A 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A A 5 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A A 5 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 5 " 0.020 2.00e-02 2.50e+03 pdb=" N1 A A 5 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A 5 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 5 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A A 5 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 19 " -0.062 2.00e-02 2.50e+03 2.85e-02 1.83e+01 pdb=" N1 C A 19 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 19 " 0.018 2.00e-02 2.50e+03 pdb=" O2 C A 19 " 0.016 2.00e-02 2.50e+03 pdb=" N3 C A 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C A 19 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 19 " -0.029 2.00e-02 2.50e+03 pdb=" C5 C A 19 " 0.008 2.00e-02 2.50e+03 pdb=" C6 C A 19 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 17 " 0.050 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G A 17 " -0.039 2.00e-02 2.50e+03 pdb=" C8 G A 17 " -0.022 2.00e-02 2.50e+03 pdb=" N7 G A 17 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 17 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G A 17 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G A 17 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G A 17 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G A 17 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A 17 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G A 17 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G A 17 " -0.012 2.00e-02 2.50e+03 ... (remaining 3351 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 613 2.71 - 3.26: 17695 3.26 - 3.80: 32139 3.80 - 4.35: 43337 4.35 - 4.90: 71330 Nonbonded interactions: 165114 Sorted by model distance: nonbonded pdb=" OH TYR B 245 " pdb=" O THR B 341 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP B 347 " pdb="MG MG B 601 " model vdw 2.170 2.170 nonbonded pdb=" O LYS D1000 " pdb=" NH1 ARG D1228 " model vdw 2.260 3.120 nonbonded pdb=" OG SER B 457 " pdb=" OD2 ASP B 462 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP B 38 " pdb=" OH TYR B 153 " model vdw 2.294 3.040 ... (remaining 165109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 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 : 0.010 0.161 20097 Z= 0.615 Angle : 1.743 14.737 27499 Z= 1.097 Chirality : 0.088 0.523 3013 Planarity : 0.007 0.098 3354 Dihedral : 17.467 179.102 7975 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 6.48 % Favored : 91.41 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2267 helix: 1.23 (0.19), residues: 633 sheet: 0.82 (0.26), residues: 346 loop : 0.05 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.005 ARG D 729 TYR 0.038 0.006 TYR C 97 PHE 0.030 0.006 PHE D 282 TRP 0.026 0.006 TRP D 429 HIS 0.014 0.004 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.01000 / 0.61 (20093) covalent geometry : angle 1.73981 / 1.10 (27493) hydrogen bonds : bond 0.18224 / 19.55 ( 789) hydrogen bonds : angle 6.73871 / 7.27 ( 2166) metal coordination : bond 0.06724 / 6.01 ( 4) metal coordination : angle 6.78155 / 12.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 SER cc_start: 0.7486 (m) cc_final: 0.7267 (t) REVERT: B 30 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5975 (tp) REVERT: B 36 MET cc_start: 0.7004 (mmm) cc_final: 0.6743 (mmp) REVERT: B 256 ASP cc_start: 0.7228 (t0) cc_final: 0.7011 (m-30) REVERT: B 258 VAL cc_start: 0.6233 (OUTLIER) cc_final: 0.5836 (t) REVERT: B 302 GLU cc_start: 0.6157 (tt0) cc_final: 0.5707 (tp30) REVERT: B 449 ARG cc_start: 0.6358 (mtp180) cc_final: 0.5972 (mtp85) REVERT: B 450 LYS cc_start: 0.6060 (mtmt) cc_final: 0.5674 (mttm) REVERT: B 550 LEU cc_start: 0.5865 (tp) cc_final: 0.5224 (tt) REVERT: C 1 MET cc_start: 0.5699 (mtt) cc_final: 0.5383 (mtt) REVERT: C 7 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6224 (mmmt) REVERT: C 94 LYS cc_start: 0.7195 (ptpt) cc_final: 0.6477 (ptpt) REVERT: C 173 TRP cc_start: 0.6836 (OUTLIER) cc_final: 0.5746 (t60) REVERT: C 221 LYS cc_start: 0.7189 (mttt) cc_final: 0.6765 (mtpp) REVERT: C 323 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7032 (tm-30) REVERT: C 390 GLU cc_start: 0.8149 (tt0) cc_final: 0.7869 (tt0) REVERT: C 454 GLN cc_start: 0.7029 (tt0) cc_final: 0.6818 (mp10) REVERT: C 487 GLU cc_start: 0.6652 (tt0) cc_final: 0.6418 (tm-30) REVERT: C 578 LYS cc_start: 0.7583 (tttp) cc_final: 0.6950 (tmmt) REVERT: C 609 MET cc_start: 0.6674 (mtt) cc_final: 0.6144 (mtm) REVERT: D 16 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5255 (mtt180) REVERT: D 47 ASP cc_start: 0.6152 (m-30) cc_final: 0.5729 (m-30) REVERT: D 90 GLU cc_start: 0.4985 (mt-10) cc_final: 0.4652 (pt0) REVERT: D 118 TYR cc_start: 0.6970 (t80) cc_final: 0.6634 (t80) REVERT: D 136 TYR cc_start: 0.8041 (p90) cc_final: 0.7515 (p90) REVERT: D 207 LYS cc_start: 0.7640 (mttt) cc_final: 0.6927 (mmtm) REVERT: D 404 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8034 (ttmt) REVERT: D 421 ASN cc_start: 0.6425 (m110) cc_final: 0.6207 (p0) REVERT: D 461 GLU cc_start: 0.7804 (tt0) cc_final: 0.7398 (tt0) REVERT: D 463 CYS cc_start: 0.7276 (t) cc_final: 0.6830 (m) REVERT: D 508 SER cc_start: 0.7360 (t) cc_final: 0.7055 (p) REVERT: D 596 LYS cc_start: 0.7761 (mmpt) cc_final: 0.6781 (mtmm) REVERT: D 745 LYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4474 (tptm) REVERT: D 853 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5944 (mm) REVERT: D 969 ASP cc_start: 0.6842 (m-30) cc_final: 0.6321 (m-30) REVERT: D 1010 HIS cc_start: 0.6728 (m90) cc_final: 0.6480 (m90) REVERT: D 1142 GLU cc_start: 0.6328 (mt-10) cc_final: 0.5900 (tt0) REVERT: D 1164 ASP cc_start: 0.7757 (t0) cc_final: 0.7542 (t0) REVERT: D 1180 LYS cc_start: 0.7404 (mmtm) cc_final: 0.6734 (mmmm) REVERT: D 1213 MET cc_start: 0.7363 (ttp) cc_final: 0.7135 (ttm) REVERT: D 1219 ILE cc_start: 0.7228 (mp) cc_final: 0.6977 (mt) outliers start: 41 outliers final: 7 residues processed: 406 average time/residue: 0.5896 time to fit residues: 270.4124 Evaluate side-chains 228 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 745 LYS Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 1102 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 ASN B 185 GLN B 205 ASN B 234 GLN B 537 HIS C 288 HIS C 470 GLN C 531 HIS D 78 HIS D 98 GLN D 195 ASN D 345 GLN D 600 HIS D 635 ASN D 976 GLN D1092 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.209575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.179277 restraints weight = 21387.041| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.76 r_work: 0.3551 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20097 Z= 0.145 Angle : 0.639 12.285 27499 Z= 0.341 Chirality : 0.045 0.256 3013 Planarity : 0.004 0.045 3354 Dihedral : 15.082 165.706 3551 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 12.35 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2267 helix: 1.57 (0.20), residues: 644 sheet: 0.77 (0.26), residues: 343 loop : 0.41 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1214 TYR 0.023 0.002 TYR B 163 PHE 0.016 0.002 PHE D 93 TRP 0.013 0.001 TRP C 257 HIS 0.009 0.001 HIS D 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (20093) covalent geometry : angle 0.63750 / 0.34 (27493) hydrogen bonds : bond 0.05361 / 5.63 ( 789) hydrogen bonds : angle 5.37313 / 6.05 ( 2166) metal coordination : bond 0.00384 / 0.35 ( 4) metal coordination : angle 2.89847 / 5.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5501 (tt) REVERT: B 34 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.6200 (tt0) REVERT: B 302 GLU cc_start: 0.5651 (tt0) cc_final: 0.5418 (tp30) REVERT: B 324 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6335 (mp10) REVERT: B 370 ARG cc_start: 0.5146 (tpp80) cc_final: 0.4603 (ppt-90) REVERT: B 422 GLU cc_start: 0.6698 (tp30) cc_final: 0.6482 (tp30) REVERT: B 450 LYS cc_start: 0.7420 (mtmt) cc_final: 0.6943 (mttm) REVERT: B 483 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.5073 (mpt) REVERT: B 488 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.4950 (ptm-80) REVERT: B 550 LEU cc_start: 0.6817 (tp) cc_final: 0.5687 (tt) REVERT: B 554 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.5515 (mp0) REVERT: C 94 LYS cc_start: 0.7234 (ptpt) cc_final: 0.6883 (ptpt) REVERT: C 173 TRP cc_start: 0.7484 (OUTLIER) cc_final: 0.6611 (t60) REVERT: C 447 ASP cc_start: 0.7322 (m-30) cc_final: 0.6583 (t0) REVERT: C 458 ASP cc_start: 0.7020 (p0) cc_final: 0.6792 (m-30) REVERT: C 507 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7139 (mtm-85) REVERT: C 528 GLN cc_start: 0.6817 (mt0) cc_final: 0.6606 (mt0) REVERT: C 578 LYS cc_start: 0.7841 (tttp) cc_final: 0.7486 (ttpt) REVERT: D 47 ASP cc_start: 0.6274 (m-30) cc_final: 0.5905 (m-30) REVERT: D 136 TYR cc_start: 0.8724 (p90) cc_final: 0.8391 (p90) REVERT: D 207 LYS cc_start: 0.8175 (mttt) cc_final: 0.7763 (mmtm) REVERT: D 356 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7982 (ttt) REVERT: D 443 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: D 596 LYS cc_start: 0.8408 (mmpt) cc_final: 0.7968 (mtmm) REVERT: D 853 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6561 (mm) REVERT: D 1213 MET cc_start: 0.7624 (ttp) cc_final: 0.7388 (ttm) outliers start: 59 outliers final: 18 residues processed: 283 average time/residue: 0.5344 time to fit residues: 171.4059 Evaluate side-chains 211 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 ASN B 205 ASN C 36 GLN C 139 ASN D 78 HIS D 98 GLN D 195 ASN D 345 GLN D 665 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.205704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.177394 restraints weight = 21587.490| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.71 r_work: 0.3528 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20097 Z= 0.123 Angle : 0.561 7.842 27499 Z= 0.301 Chirality : 0.043 0.232 3013 Planarity : 0.004 0.042 3354 Dihedral : 14.243 165.463 3533 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.78 % Allowed : 14.30 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2267 helix: 1.64 (0.20), residues: 642 sheet: 0.85 (0.27), residues: 327 loop : 0.41 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1214 TYR 0.017 0.001 TYR B 238 PHE 0.013 0.002 PHE C 155 TRP 0.013 0.001 TRP D 429 HIS 0.004 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20093) covalent geometry : angle 0.56022 / 0.30 (27493) hydrogen bonds : bond 0.04619 / 4.86 ( 789) hydrogen bonds : angle 5.04385 / 5.67 ( 2166) metal coordination : bond 0.00441 / 0.39 ( 4) metal coordination : angle 2.36179 / 4.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0027 (mpp) cc_final: -0.0473 (mtt) REVERT: B 33 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5582 (tp) REVERT: B 225 ARG cc_start: 0.4596 (OUTLIER) cc_final: 0.4292 (ttt90) REVERT: B 302 GLU cc_start: 0.5643 (tt0) cc_final: 0.5374 (tp30) REVERT: B 370 ARG cc_start: 0.5039 (tpp80) cc_final: 0.4455 (ppt-90) REVERT: B 426 LYS cc_start: 0.7233 (mttm) cc_final: 0.6728 (mppt) REVERT: B 450 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6970 (mttm) REVERT: B 483 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5334 (mpt) REVERT: B 488 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.5011 (ptm-80) REVERT: C 94 LYS cc_start: 0.7267 (ptpt) cc_final: 0.6944 (ptpt) REVERT: C 173 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.6517 (t60) REVERT: C 180 MET cc_start: 0.7943 (mtm) cc_final: 0.7628 (mtp) REVERT: C 447 ASP cc_start: 0.7306 (m-30) cc_final: 0.6623 (t0) REVERT: C 458 ASP cc_start: 0.7417 (p0) cc_final: 0.6944 (m-30) REVERT: C 507 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7293 (mtm-85) REVERT: C 529 LYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5209 (ptpp) REVERT: C 578 LYS cc_start: 0.7935 (tttp) cc_final: 0.7582 (ttpt) REVERT: D 47 ASP cc_start: 0.6356 (m-30) cc_final: 0.5966 (m-30) REVERT: D 136 TYR cc_start: 0.8804 (p90) cc_final: 0.8482 (p90) REVERT: D 439 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7227 (mtp180) REVERT: D 596 LYS cc_start: 0.8463 (mmpt) cc_final: 0.8023 (mtmm) REVERT: D 853 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6616 (mm) REVERT: D 1080 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (tttm) REVERT: D 1179 ASN cc_start: 0.7870 (m110) cc_final: 0.7296 (t0) REVERT: D 1217 ASP cc_start: 0.6857 (p0) cc_final: 0.6198 (m-30) outliers start: 54 outliers final: 17 residues processed: 243 average time/residue: 0.5869 time to fit residues: 161.7686 Evaluate side-chains 204 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1219 ILE Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 454 GLN D 78 HIS D 195 ASN D 421 ASN D 693 GLN D 879 ASN D 933 GLN D 995 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.201693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.165930 restraints weight = 21618.686| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.17 r_work: 0.3477 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20097 Z= 0.123 Angle : 0.546 8.326 27499 Z= 0.291 Chirality : 0.043 0.246 3013 Planarity : 0.004 0.054 3354 Dihedral : 14.095 166.852 3531 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.83 % Allowed : 15.33 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2267 helix: 1.64 (0.20), residues: 631 sheet: 0.88 (0.27), residues: 328 loop : 0.34 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 364 TYR 0.020 0.002 TYR D 97 PHE 0.017 0.002 PHE C 155 TRP 0.015 0.001 TRP D 695 HIS 0.006 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (20093) covalent geometry : angle 0.54453 / 0.29 (27493) hydrogen bonds : bond 0.04249 / 4.51 ( 789) hydrogen bonds : angle 4.89794 / 5.50 ( 2166) metal coordination : bond 0.00401 / 0.36 ( 4) metal coordination : angle 2.60761 / 5.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0260 (mpp) cc_final: -0.0165 (mtt) REVERT: B 162 LEU cc_start: 0.6813 (mt) cc_final: 0.6371 (mm) REVERT: B 225 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.4254 (ttt90) REVERT: B 245 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.5329 (t80) REVERT: B 302 GLU cc_start: 0.5759 (tt0) cc_final: 0.5474 (tp30) REVERT: B 324 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6650 (mp10) REVERT: B 339 LEU cc_start: 0.8018 (tt) cc_final: 0.7798 (tm) REVERT: B 370 ARG cc_start: 0.5225 (tpp80) cc_final: 0.4611 (ppt-90) REVERT: B 450 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7117 (mttm) REVERT: B 470 MET cc_start: 0.4728 (mtp) cc_final: 0.3871 (ttm) REVERT: B 483 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5584 (mpt) REVERT: B 488 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5115 (ptm-80) REVERT: C 94 LYS cc_start: 0.7288 (ptpt) cc_final: 0.6972 (ptpt) REVERT: C 173 TRP cc_start: 0.7719 (OUTLIER) cc_final: 0.6524 (t60) REVERT: C 180 MET cc_start: 0.7994 (mtm) cc_final: 0.7695 (mtp) REVERT: C 447 ASP cc_start: 0.7437 (m-30) cc_final: 0.6672 (t0) REVERT: C 458 ASP cc_start: 0.7723 (p0) cc_final: 0.7025 (m-30) REVERT: C 507 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: C 529 LYS cc_start: 0.5711 (OUTLIER) cc_final: 0.5208 (ptpp) REVERT: C 578 LYS cc_start: 0.8011 (tttp) cc_final: 0.7716 (ttpt) REVERT: D 47 ASP cc_start: 0.6536 (m-30) cc_final: 0.6059 (m-30) REVERT: D 136 TYR cc_start: 0.8943 (p90) cc_final: 0.8637 (p90) REVERT: D 443 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: D 596 LYS cc_start: 0.8594 (mmpt) cc_final: 0.8055 (mtmm) REVERT: D 1080 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8274 (tttm) REVERT: D 1096 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7145 (mtm-85) REVERT: D 1102 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.3780 (pp20) REVERT: D 1179 ASN cc_start: 0.8042 (m110) cc_final: 0.7482 (t0) REVERT: D 1217 ASP cc_start: 0.7218 (p0) cc_final: 0.6539 (m-30) outliers start: 55 outliers final: 17 residues processed: 228 average time/residue: 0.5616 time to fit residues: 144.5301 Evaluate side-chains 203 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1219 ILE Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 138 optimal weight: 0.0470 chunk 204 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 218 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 191 optimal weight: 0.0870 chunk 129 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN C 454 GLN D 78 HIS D 195 ASN D 302 GLN D 879 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.203635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.169620 restraints weight = 21540.956| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.97 r_work: 0.3530 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20097 Z= 0.102 Angle : 0.505 9.975 27499 Z= 0.269 Chirality : 0.041 0.238 3013 Planarity : 0.004 0.042 3354 Dihedral : 14.009 170.549 3529 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 16.10 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2267 helix: 1.77 (0.20), residues: 632 sheet: 0.78 (0.26), residues: 345 loop : 0.33 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 364 TYR 0.020 0.001 TYR B 233 PHE 0.015 0.001 PHE C 156 TRP 0.017 0.001 TRP D 695 HIS 0.005 0.001 HIS D 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (20093) covalent geometry : angle 0.50405 / 0.27 (27493) hydrogen bonds : bond 0.03915 / 4.13 ( 789) hydrogen bonds : angle 4.73891 / 5.31 ( 2166) metal coordination : bond 0.00321 / 0.29 ( 4) metal coordination : angle 2.40017 / 4.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: -0.0072 (mpp) cc_final: -0.0348 (mtt) REVERT: B 22 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6520 (tp) REVERT: B 162 LEU cc_start: 0.6811 (mt) cc_final: 0.6370 (mm) REVERT: B 245 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.5775 (t80) REVERT: B 302 GLU cc_start: 0.5677 (tt0) cc_final: 0.5467 (tp30) REVERT: B 324 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: B 364 ARG cc_start: 0.7053 (tpm-80) cc_final: 0.6809 (tpm-80) REVERT: B 370 ARG cc_start: 0.5341 (tpp80) cc_final: 0.4622 (ppt-90) REVERT: B 450 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7025 (mttm) REVERT: B 470 MET cc_start: 0.5085 (mtp) cc_final: 0.4119 (ttm) REVERT: B 483 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5412 (mpt) REVERT: B 488 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5001 (ptm-80) REVERT: C 65 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6829 (ttm-80) REVERT: C 94 LYS cc_start: 0.7159 (ptpt) cc_final: 0.6934 (ptpt) REVERT: C 180 MET cc_start: 0.7951 (mtm) cc_final: 0.7669 (mtp) REVERT: C 458 ASP cc_start: 0.7691 (p0) cc_final: 0.7054 (m-30) REVERT: C 507 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7328 (mtm-85) REVERT: C 529 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5374 (ptpp) REVERT: C 578 LYS cc_start: 0.8063 (tttp) cc_final: 0.7747 (ttpt) REVERT: D 47 ASP cc_start: 0.6220 (m-30) cc_final: 0.5890 (m-30) REVERT: D 97 TYR cc_start: 0.6854 (t80) cc_final: 0.6556 (t80) REVERT: D 136 TYR cc_start: 0.8892 (p90) cc_final: 0.8611 (p90) REVERT: D 232 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.4926 (tm130) REVERT: D 439 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: D 443 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: D 596 LYS cc_start: 0.8502 (mmpt) cc_final: 0.8063 (mtmm) REVERT: D 1080 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (tttm) REVERT: D 1096 ARG cc_start: 0.7407 (mtt90) cc_final: 0.7040 (mtm-85) REVERT: D 1102 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.3720 (pp20) REVERT: D 1179 ASN cc_start: 0.7891 (m110) cc_final: 0.7385 (t0) REVERT: D 1217 ASP cc_start: 0.7078 (p0) cc_final: 0.6455 (m-30) outliers start: 53 outliers final: 18 residues processed: 229 average time/residue: 0.6427 time to fit residues: 165.9334 Evaluate side-chains 206 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1219 ILE Chi-restraints excluded: chain D residue 1221 THR Chi-restraints excluded: chain D residue 1228 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 230 optimal weight: 40.0000 chunk 154 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 454 GLN D 78 HIS D 195 ASN D 898 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.201225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.167252 restraints weight = 21382.939| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.98 r_work: 0.3498 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20097 Z= 0.117 Angle : 0.523 8.099 27499 Z= 0.276 Chirality : 0.042 0.242 3013 Planarity : 0.004 0.044 3354 Dihedral : 13.978 170.002 3527 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.52 % Allowed : 16.56 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2267 helix: 1.69 (0.20), residues: 640 sheet: 0.86 (0.27), residues: 329 loop : 0.31 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 785 TYR 0.024 0.001 TYR B 163 PHE 0.017 0.002 PHE B 127 TRP 0.020 0.001 TRP D 695 HIS 0.006 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20093) covalent geometry : angle 0.52106 / 0.28 (27493) hydrogen bonds : bond 0.03976 / 4.22 ( 789) hydrogen bonds : angle 4.73375 / 5.29 ( 2166) metal coordination : bond 0.00346 / 0.31 ( 4) metal coordination : angle 2.78630 / 5.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0101 (mpp) cc_final: -0.0218 (mtt) REVERT: B 39 ILE cc_start: 0.4824 (mt) cc_final: 0.4529 (mt) REVERT: B 162 LEU cc_start: 0.6941 (mt) cc_final: 0.6461 (mm) REVERT: B 245 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 302 GLU cc_start: 0.5646 (tt0) cc_final: 0.5333 (tp30) REVERT: B 324 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: B 364 ARG cc_start: 0.7026 (tpm-80) cc_final: 0.6346 (tpm170) REVERT: B 450 LYS cc_start: 0.7450 (mtmt) cc_final: 0.7048 (mttm) REVERT: B 470 MET cc_start: 0.5323 (mtp) cc_final: 0.4487 (ttm) REVERT: B 483 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5636 (mpt) REVERT: B 488 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5075 (ptm-80) REVERT: C 65 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.6885 (ttm-80) REVERT: C 180 MET cc_start: 0.7955 (mtm) cc_final: 0.7635 (mtp) REVERT: C 279 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7017 (mp0) REVERT: C 458 ASP cc_start: 0.7786 (p0) cc_final: 0.7135 (m-30) REVERT: C 507 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7325 (mtm-85) REVERT: C 578 LYS cc_start: 0.8120 (tttp) cc_final: 0.7807 (ttpt) REVERT: D 596 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8097 (mttt) REVERT: D 785 ARG cc_start: 0.6781 (ttp80) cc_final: 0.6514 (ptm160) REVERT: D 1080 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8253 (tttm) REVERT: D 1096 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7028 (mtm-85) REVERT: D 1102 GLU cc_start: 0.4658 (OUTLIER) cc_final: 0.3895 (pp20) REVERT: D 1179 ASN cc_start: 0.7937 (m110) cc_final: 0.7444 (t0) outliers start: 49 outliers final: 20 residues processed: 216 average time/residue: 0.6874 time to fit residues: 168.3244 Evaluate side-chains 203 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 945 SER Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 39 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 190 optimal weight: 0.1980 chunk 174 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 454 GLN D 78 HIS D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.202932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.174649 restraints weight = 21071.492| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.59 r_work: 0.3491 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20097 Z= 0.138 Angle : 0.544 8.295 27499 Z= 0.287 Chirality : 0.043 0.239 3013 Planarity : 0.004 0.049 3354 Dihedral : 13.985 167.605 3527 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.52 % Allowed : 17.08 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2267 helix: 1.60 (0.20), residues: 641 sheet: 0.71 (0.27), residues: 327 loop : 0.23 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 370 TYR 0.021 0.002 TYR D 97 PHE 0.018 0.002 PHE C 155 TRP 0.017 0.001 TRP D 429 HIS 0.008 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (20093) covalent geometry : angle 0.54234 / 0.29 (27493) hydrogen bonds : bond 0.04176 / 4.44 ( 789) hydrogen bonds : angle 4.82560 / 5.35 ( 2166) metal coordination : bond 0.00331 / 0.30 ( 4) metal coordination : angle 2.81549 / 5.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0275 (mpp) cc_final: -0.0116 (mtt) REVERT: B 162 LEU cc_start: 0.7021 (mt) cc_final: 0.6561 (mm) REVERT: B 245 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.5352 (t80) REVERT: B 302 GLU cc_start: 0.5728 (tt0) cc_final: 0.5368 (tp30) REVERT: B 324 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6591 (mp10) REVERT: B 364 ARG cc_start: 0.7070 (tpm-80) cc_final: 0.6386 (tpm170) REVERT: B 450 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7213 (mttm) REVERT: B 451 ASN cc_start: 0.8047 (t0) cc_final: 0.7599 (t0) REVERT: B 475 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.6159 (p0) REVERT: B 483 MET cc_start: 0.6177 (mpt) cc_final: 0.5828 (mpt) REVERT: B 488 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.5074 (ptm-80) REVERT: B 534 GLU cc_start: 0.6026 (mm-30) cc_final: 0.5670 (mt-10) REVERT: C 65 ARG cc_start: 0.7291 (mtt-85) cc_final: 0.6960 (ttm-80) REVERT: C 180 MET cc_start: 0.7781 (mtm) cc_final: 0.7481 (mtp) REVERT: C 279 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7078 (mp0) REVERT: C 458 ASP cc_start: 0.7821 (p0) cc_final: 0.7132 (m-30) REVERT: C 507 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7547 (mtm-85) REVERT: C 578 LYS cc_start: 0.8192 (tttp) cc_final: 0.7900 (ttpt) REVERT: D 98 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5611 (mt0) REVERT: D 232 GLN cc_start: 0.5707 (OUTLIER) cc_final: 0.4994 (tm130) REVERT: D 439 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7794 (mtp180) REVERT: D 596 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8117 (mtmm) REVERT: D 729 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6828 (ttt90) REVERT: D 1080 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8296 (tttm) REVERT: D 1096 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7070 (mtp85) REVERT: D 1102 GLU cc_start: 0.4761 (OUTLIER) cc_final: 0.3943 (pp20) REVERT: D 1179 ASN cc_start: 0.7924 (m110) cc_final: 0.7501 (t0) outliers start: 49 outliers final: 25 residues processed: 216 average time/residue: 0.6762 time to fit residues: 165.0448 Evaluate side-chains 212 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 945 SER Chi-restraints excluded: chain D residue 999 THR Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 51 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 427 GLN C 454 GLN D 78 HIS D 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.199870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165133 restraints weight = 21394.658| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.95 r_work: 0.3485 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20097 Z= 0.113 Angle : 0.521 8.142 27499 Z= 0.276 Chirality : 0.041 0.239 3013 Planarity : 0.004 0.046 3354 Dihedral : 13.960 169.477 3527 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.26 % Allowed : 17.75 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2267 helix: 1.73 (0.20), residues: 634 sheet: 0.72 (0.27), residues: 329 loop : 0.26 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 364 TYR 0.014 0.001 TYR B 163 PHE 0.017 0.001 PHE B 127 TRP 0.017 0.001 TRP D 429 HIS 0.005 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20093) covalent geometry : angle 0.51981 / 0.28 (27493) hydrogen bonds : bond 0.03909 / 4.13 ( 789) hydrogen bonds : angle 4.72860 / 5.22 ( 2166) metal coordination : bond 0.00298 / 0.27 ( 4) metal coordination : angle 2.70145 / 5.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0419 (mpp) cc_final: 0.0111 (mtt) REVERT: B 162 LEU cc_start: 0.7062 (mt) cc_final: 0.6603 (mm) REVERT: B 245 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5224 (t80) REVERT: B 261 THR cc_start: 0.5982 (t) cc_final: 0.5768 (m) REVERT: B 302 GLU cc_start: 0.5547 (tt0) cc_final: 0.5300 (tp30) REVERT: B 324 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: B 364 ARG cc_start: 0.6921 (tpm-80) cc_final: 0.6504 (tpp-160) REVERT: B 450 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7221 (mttm) REVERT: B 451 ASN cc_start: 0.8048 (t0) cc_final: 0.7581 (t0) REVERT: B 470 MET cc_start: 0.4808 (mtp) cc_final: 0.4325 (ttm) REVERT: B 475 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6229 (p0) REVERT: B 483 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5866 (mpt) REVERT: B 488 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5068 (ptm-80) REVERT: B 534 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5736 (mt-10) REVERT: C 65 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6839 (ttm-80) REVERT: C 106 GLU cc_start: 0.7658 (pm20) cc_final: 0.7399 (pm20) REVERT: C 180 MET cc_start: 0.7895 (mtm) cc_final: 0.7600 (mtp) REVERT: C 458 ASP cc_start: 0.7831 (p0) cc_final: 0.7129 (m-30) REVERT: C 507 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7478 (mtm-85) REVERT: C 578 LYS cc_start: 0.8215 (tttp) cc_final: 0.7928 (ttpt) REVERT: D 232 GLN cc_start: 0.5471 (OUTLIER) cc_final: 0.4791 (tm130) REVERT: D 439 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7812 (mtp180) REVERT: D 596 LYS cc_start: 0.8492 (mmpt) cc_final: 0.8067 (mtmm) REVERT: D 729 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6801 (ttt90) REVERT: D 785 ARG cc_start: 0.6850 (ttp80) cc_final: 0.6472 (ptm160) REVERT: D 1080 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8316 (tttm) REVERT: D 1096 ARG cc_start: 0.7488 (mtt90) cc_final: 0.7078 (mtp85) REVERT: D 1102 GLU cc_start: 0.4802 (OUTLIER) cc_final: 0.4001 (pp20) REVERT: D 1179 ASN cc_start: 0.7933 (m110) cc_final: 0.7516 (t0) outliers start: 44 outliers final: 21 residues processed: 220 average time/residue: 0.6611 time to fit residues: 164.9233 Evaluate side-chains 205 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 945 SER Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1221 THR Chi-restraints excluded: chain D residue 1228 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 50 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.2307 > 50:) chunk 145 optimal weight: 0.0060 chunk 68 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 259 HIS D 78 HIS D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.203533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.170020 restraints weight = 21319.927| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.91 r_work: 0.3540 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20097 Z= 0.093 Angle : 0.490 7.926 27499 Z= 0.262 Chirality : 0.040 0.238 3013 Planarity : 0.004 0.042 3354 Dihedral : 13.935 173.420 3527 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.75 % Allowed : 18.21 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2267 helix: 1.83 (0.21), residues: 633 sheet: 0.66 (0.26), residues: 356 loop : 0.31 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1214 TYR 0.013 0.001 TYR B 163 PHE 0.013 0.001 PHE C 155 TRP 0.017 0.001 TRP D 429 HIS 0.005 0.001 HIS D 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (20093) covalent geometry : angle 0.48844 / 0.26 (27493) hydrogen bonds : bond 0.03549 / 3.75 ( 789) hydrogen bonds : angle 4.56511 / 5.03 ( 2166) metal coordination : bond 0.00299 / 0.27 ( 4) metal coordination : angle 2.53676 / 4.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 LEU cc_start: 0.7070 (mt) cc_final: 0.6673 (mm) REVERT: B 245 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5231 (t80) REVERT: B 324 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6687 (mp10) REVERT: B 450 LYS cc_start: 0.7454 (mtmt) cc_final: 0.7063 (mttm) REVERT: B 470 MET cc_start: 0.4700 (mtp) cc_final: 0.4398 (ttm) REVERT: B 483 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5909 (mpt) REVERT: B 488 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5084 (ptm-80) REVERT: B 534 GLU cc_start: 0.5989 (mm-30) cc_final: 0.5706 (mt-10) REVERT: C 106 GLU cc_start: 0.7646 (pm20) cc_final: 0.7385 (pm20) REVERT: C 180 MET cc_start: 0.7904 (mtm) cc_final: 0.7633 (mtp) REVERT: C 458 ASP cc_start: 0.7773 (p0) cc_final: 0.7198 (m-30) REVERT: C 507 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7446 (mtm-85) REVERT: C 529 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5815 (ptpp) REVERT: C 578 LYS cc_start: 0.8174 (tttp) cc_final: 0.7953 (ttpt) REVERT: D 47 ASP cc_start: 0.6486 (m-30) cc_final: 0.6238 (m-30) REVERT: D 232 GLN cc_start: 0.5389 (OUTLIER) cc_final: 0.4741 (tm130) REVERT: D 439 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7798 (mtp180) REVERT: D 596 LYS cc_start: 0.8387 (mmpt) cc_final: 0.7979 (mttt) REVERT: D 729 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6806 (ttt90) REVERT: D 1080 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8271 (tttm) REVERT: D 1096 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7021 (mtp85) REVERT: D 1102 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4068 (pp20) REVERT: D 1179 ASN cc_start: 0.7867 (m110) cc_final: 0.7465 (t0) REVERT: D 1217 ASP cc_start: 0.7429 (p0) cc_final: 0.6696 (m-30) outliers start: 34 outliers final: 15 residues processed: 211 average time/residue: 0.6405 time to fit residues: 153.0562 Evaluate side-chains 201 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 945 SER Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1102 GLU Chi-restraints excluded: chain D residue 1228 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN C 574 ASN D 78 HIS D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.198701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.171772 restraints weight = 21272.752| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.61 r_work: 0.3466 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20097 Z= 0.185 Angle : 0.612 9.269 27499 Z= 0.319 Chirality : 0.044 0.245 3013 Planarity : 0.005 0.055 3354 Dihedral : 13.949 166.846 3527 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.44 % Allowed : 19.03 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2267 helix: 1.55 (0.20), residues: 634 sheet: 0.58 (0.27), residues: 335 loop : 0.19 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1214 TYR 0.016 0.002 TYR B 163 PHE 0.019 0.002 PHE C 155 TRP 0.014 0.002 TRP D 429 HIS 0.011 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (20093) covalent geometry : angle 0.60996 / 0.32 (27493) hydrogen bonds : bond 0.04479 / 4.75 ( 789) hydrogen bonds : angle 4.89615 / 5.36 ( 2166) metal coordination : bond 0.00334 / 0.31 ( 4) metal coordination : angle 3.07482 / 5.91 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 GLU cc_start: 0.5886 (mp0) cc_final: 0.5590 (mp0) REVERT: B 133 GLU cc_start: 0.5665 (pm20) cc_final: 0.5313 (pm20) REVERT: B 245 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5116 (t80) REVERT: B 324 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6675 (mp10) REVERT: B 364 ARG cc_start: 0.6843 (tpm-80) cc_final: 0.6522 (tpm170) REVERT: B 450 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7195 (mttm) REVERT: B 451 ASN cc_start: 0.8036 (t0) cc_final: 0.7586 (t0) REVERT: B 470 MET cc_start: 0.4944 (mtp) cc_final: 0.4546 (ttm) REVERT: B 483 MET cc_start: 0.6511 (mpt) cc_final: 0.6260 (mpt) REVERT: B 488 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5081 (ptm-80) REVERT: B 534 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5778 (mt-10) REVERT: C 106 GLU cc_start: 0.7672 (pm20) cc_final: 0.7387 (pm20) REVERT: C 174 PHE cc_start: 0.7298 (m-80) cc_final: 0.7097 (m-10) REVERT: C 180 MET cc_start: 0.7807 (mtm) cc_final: 0.7519 (mtp) REVERT: C 458 ASP cc_start: 0.7785 (p0) cc_final: 0.7158 (m-30) REVERT: C 507 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7853 (mtm-85) REVERT: C 578 LYS cc_start: 0.8299 (tttp) cc_final: 0.8018 (ttpt) REVERT: D 47 ASP cc_start: 0.6943 (m-30) cc_final: 0.6574 (m-30) REVERT: D 232 GLN cc_start: 0.5685 (OUTLIER) cc_final: 0.4965 (tm130) REVERT: D 439 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: D 596 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8081 (mptt) REVERT: D 729 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6834 (ttt90) REVERT: D 1096 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7113 (mtp85) REVERT: D 1179 ASN cc_start: 0.7976 (m110) cc_final: 0.7582 (t0) outliers start: 28 outliers final: 16 residues processed: 206 average time/residue: 0.5894 time to fit residues: 137.6304 Evaluate side-chains 200 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 723 ARG Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 945 SER Chi-restraints excluded: chain D residue 1048 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 83 optimal weight: 0.0470 chunk 221 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN ** B 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN D 78 HIS D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.200270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.169458 restraints weight = 21272.774| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.74 r_work: 0.3491 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20097 Z= 0.128 Angle : 0.543 8.854 27499 Z= 0.287 Chirality : 0.042 0.236 3013 Planarity : 0.004 0.047 3354 Dihedral : 13.855 168.575 3527 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.59 % Allowed : 19.34 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2267 helix: 1.66 (0.20), residues: 634 sheet: 0.58 (0.27), residues: 343 loop : 0.20 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 364 TYR 0.015 0.001 TYR C 580 PHE 0.017 0.002 PHE C 155 TRP 0.017 0.001 TRP D 429 HIS 0.006 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20093) covalent geometry : angle 0.54170 / 0.29 (27493) hydrogen bonds : bond 0.04031 / 4.26 ( 789) hydrogen bonds : angle 4.76277 / 5.23 ( 2166) metal coordination : bond 0.00297 / 0.27 ( 4) metal coordination : angle 2.71791 / 5.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.23 seconds wall clock time: 96 minutes 19.41 seconds (5779.41 seconds total)