Starting phenix.real_space_refine on Fri Aug 7 08:46:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.map" model { file = "/net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wxj_66348/08_2026/9wxj_66348.cif" } resolution = 2.7 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= 0.029 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 78 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 12255 2.51 5 N 3496 2.21 5 O 4015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.01s 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: 19909 Number of models: 1 Model: "" Number of chains: 9 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: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3895 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 15, 'TRANS': 462} Chain breaks: 3 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: 9432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9432 Classifications: {'peptide': 1194} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1133} Chain breaks: 2 Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 30} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} 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 12095 SG CYS D 338 56.247 85.215 84.735 1.00 62.83 S ATOM 12138 SG CYS D 344 57.734 86.151 88.003 1.00 63.77 S ATOM 12188 SG CYS D 351 56.172 88.798 85.919 1.00 52.30 S ATOM 12207 SG CYS D 354 53.970 86.151 87.374 1.00 52.13 S Time building chain proxies: 3.55, per 1000 atoms: 0.18 Number of scatterers: 19909 At special positions: 0 Unit cell: (112.548, 120.516, 176.292, 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 78 15.00 Mg 2 11.99 O 4015 8.00 N 3496 7.00 C 12255 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: 1.87 Conformation dependent library (CDL) restraints added in 782.3 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 344 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 338 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 354 " Number of angles added : 6 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 38 sheets defined 35.1% alpha, 22.3% beta 31 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'B' and resid 21 through 39 removed outlier: 3.685A pdb=" N MET B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.841A 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: 3.999A 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 296 Processing helix chain 'B' and resid 299 through 327 removed outlier: 3.562A pdb=" N GLY B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.279A 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 357 through 373 removed outlier: 3.620A 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: 3.720A pdb=" N LYS B 426 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 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 499 removed outlier: 3.934A pdb=" N ILE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'B' and resid 521 through 542 Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'C' and resid 43 through 65 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.512A pdb=" N SER C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.661A pdb=" N PHE C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 245 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: 3.970A 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: 3.501A 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 122 through 126 removed outlier: 4.181A pdb=" N TYR D 125 " --> pdb=" O GLY D 122 " (cutoff:3.500A) 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 removed outlier: 3.501A pdb=" N PHE D 243 " --> pdb=" O THR D 240 " (cutoff:3.500A) 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: 3.512A 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 532 through 536 removed outlier: 3.752A pdb=" N THR D 535 " --> pdb=" O ASP D 532 " (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 682 through 691 removed outlier: 3.573A 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 796 Processing helix chain 'D' and resid 800 through 804 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 900 through 904 removed outlier: 3.575A pdb=" N ARG D 904 " --> pdb=" O LYS D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 928 removed outlier: 3.704A pdb=" N ILE D 927 " --> pdb=" O PRO D 923 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 928 " --> pdb=" O ASP D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 932 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 966 through 970 Processing helix chain 'D' and resid 1021 through 1024 Processing helix chain 'D' and resid 1047 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: 3.604A 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: 4.189A 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: 5.631A pdb=" N THR B 117 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B 128 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.427A 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: 4.526A pdb=" N ASP B 212 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.445A pdb=" N LYS B 259 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 340 through 343 removed outlier: 6.251A pdb=" N ILE B 350 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 391 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA B 431 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER B 393 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLN B 433 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 395 " --> pdb=" O GLN B 433 " (cutoff:3.500A) 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: 6.351A pdb=" N LYS C 13 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.171A 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 122 removed outlier: 10.852A pdb=" N ARG C 117 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ILE C 134 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 10.063A pdb=" N ARG C 119 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ARG C 132 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR C 121 " --> pdb=" O LYS C 130 " (cutoff:3.500A) 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: 5.314A pdb=" N THR C 437 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 431 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 237 through 239 removed outlier: 6.854A pdb=" N PHE C 238 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL C 392 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N LYS C 383 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASP C 375 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN C 385 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 4.590A 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 306 through 307 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 506 through 512 removed outlier: 6.945A pdb=" N VAL C 547 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR C 511 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 545 " --> pdb=" O TYR C 511 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 518 Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.471A pdb=" N ARG D 166 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.471A pdb=" N ARG D 166 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR D 22 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN D 215 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 24 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE D 213 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 32 through 42 removed outlier: 5.077A pdb=" N GLU D 35 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N TYR D 157 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN D 52 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLU D 159 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN D 54 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 366 through 368 Processing sheet with id=AC4, first strand: chain 'D' and resid 366 through 368 removed outlier: 3.557A pdb=" N GLY D 273 " --> pdb=" O THR D 465 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 281 through 282 removed outlier: 6.382A pdb=" N HIS D 301 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE D 406 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 281 through 282 removed outlier: 5.555A pdb=" N ALA D 387 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N GLY D 398 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE D 385 " --> pdb=" O GLY D 398 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N LEU D 400 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N GLN D 383 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N SER D 402 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N LYS D 381 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 518 through 519 Processing sheet with id=AC8, first strand: chain 'D' and resid 523 through 526 Processing sheet with id=AC9, first strand: chain 'D' and resid 537 through 538 Processing sheet with id=AD1, first strand: chain 'D' and resid 914 through 916 removed outlier: 5.499A pdb=" N HIS D 565 " --> pdb=" O ASN D1045 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 920 through 921 removed outlier: 5.499A pdb=" N HIS D 565 " --> pdb=" O ASN D1045 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 582 through 585 removed outlier: 4.291A pdb=" N GLY D 584 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS D 596 " --> pdb=" O ARG D1027 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 602 through 603 Processing sheet with id=AD5, first strand: chain 'D' and resid 639 through 641 Processing sheet with id=AD6, first strand: chain 'D' and resid 776 through 777 removed outlier: 6.871A pdb=" N ILE D 651 " --> pdb=" O MET D 666 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 650 " --> pdb=" O PHE D 843 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 674 through 676 Processing sheet with id=AD8, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AD9, first strand: chain 'D' and resid 825 through 826 Processing sheet with id=AE1, first strand: chain 'D' and resid 893 through 895 Processing sheet with id=AE2, first strand: chain 'D' and resid 955 through 957 764 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4076 1.33 - 1.45: 6234 1.45 - 1.58: 9947 1.58 - 1.70: 154 1.70 - 1.82: 95 Bond restraints: 20506 Sorted by residual: bond pdb=" N9 G A 39 " pdb=" C8 G A 39 " ideal model delta sigma weight residual 1.374 1.456 -0.082 7.00e-03 2.04e+04 1.38e+02 bond pdb=" C5 G A 39 " pdb=" C4 G A 39 " ideal model delta sigma weight residual 1.379 1.454 -0.075 7.00e-03 2.04e+04 1.13e+02 bond pdb=" C6 G A 39 " pdb=" N1 G A 39 " ideal model delta sigma weight residual 1.391 1.458 -0.067 7.00e-03 2.04e+04 9.07e+01 bond pdb=" N1 G A 39 " pdb=" C2 G A 39 " ideal model delta sigma weight residual 1.373 1.449 -0.076 8.00e-03 1.56e+04 9.07e+01 bond pdb=" C8 G A 39 " pdb=" N7 G A 39 " ideal model delta sigma weight residual 1.305 1.359 -0.054 6.00e-03 2.78e+04 7.95e+01 ... (remaining 20501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 27382 4.10 - 8.19: 683 8.19 - 12.29: 42 12.29 - 16.39: 8 16.39 - 20.49: 2 Bond angle restraints: 28117 Sorted by residual: angle pdb=" O3' C A 30 " pdb=" P U A 31 " pdb=" O5' U A 31 " ideal model delta sigma weight residual 104.00 83.51 20.49 1.90e+00 2.77e-01 1.16e+02 angle pdb=" O3' A A 5 " pdb=" P A A 6 " pdb=" O5' A A 6 " ideal model delta sigma weight residual 104.00 85.85 18.15 1.90e+00 2.77e-01 9.12e+01 angle pdb=" O4' A A 27 " pdb=" C1' A A 27 " pdb=" N9 A A 27 " ideal model delta sigma weight residual 108.20 115.31 -7.11 8.00e-01 1.56e+00 7.89e+01 angle pdb=" O3' U A 12 " pdb=" P C A 13 " pdb=" O5' C A 13 " ideal model delta sigma weight residual 104.00 87.68 16.32 1.90e+00 2.77e-01 7.38e+01 angle pdb=" O4' C A 13 " pdb=" C1' C A 13 " pdb=" N1 C A 13 " ideal model delta sigma weight residual 108.20 115.06 -6.86 8.00e-01 1.56e+00 7.35e+01 ... (remaining 28112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 11725 29.78 - 59.57: 559 59.57 - 89.35: 160 89.35 - 119.14: 3 119.14 - 148.92: 3 Dihedral angle restraints: 12450 sinusoidal: 5830 harmonic: 6620 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 232.00 83.08 148.92 1 1.70e+01 3.46e-03 6.17e+01 dihedral pdb=" CA SER D 706 " pdb=" C SER D 706 " pdb=" N ALA D 707 " pdb=" CA ALA D 707 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+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 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2879 0.154 - 0.309: 198 0.309 - 0.463: 9 0.463 - 0.618: 4 0.618 - 0.772: 2 Chirality restraints: 3092 Sorted by residual: chirality pdb=" P U A 31 " pdb=" OP1 U A 31 " pdb=" OP2 U A 31 " pdb=" O5' U A 31 " both_signs ideal model delta sigma weight residual True 2.41 -1.64 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" P A A 6 " pdb=" OP1 A A 6 " pdb=" OP2 A A 6 " pdb=" O5' A A 6 " both_signs ideal model delta sigma weight residual True 2.41 -1.76 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P C E 17 " pdb=" OP1 C E 17 " pdb=" OP2 C E 17 " pdb=" O5' C E 17 " both_signs ideal model delta sigma weight residual True 2.41 -1.82 0.59 2.00e-01 2.50e+01 8.63e+00 ... (remaining 3089 not shown) Planarity restraints: 3386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A E 32 " 0.116 2.00e-02 2.50e+03 4.94e-02 6.72e+01 pdb=" N9 A E 32 " -0.094 2.00e-02 2.50e+03 pdb=" C8 A E 32 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A E 32 " -0.022 2.00e-02 2.50e+03 pdb=" C5 A E 32 " -0.011 2.00e-02 2.50e+03 pdb=" C6 A E 32 " 0.015 2.00e-02 2.50e+03 pdb=" N6 A E 32 " 0.043 2.00e-02 2.50e+03 pdb=" N1 A E 32 " 0.020 2.00e-02 2.50e+03 pdb=" C2 A E 32 " -0.022 2.00e-02 2.50e+03 pdb=" N3 A E 32 " -0.031 2.00e-02 2.50e+03 pdb=" C4 A E 32 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 13 " -0.115 2.00e-02 2.50e+03 5.32e-02 6.36e+01 pdb=" N1 C A 13 " 0.074 2.00e-02 2.50e+03 pdb=" C2 C A 13 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 13 " 0.021 2.00e-02 2.50e+03 pdb=" N3 C A 13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 13 " -0.020 2.00e-02 2.50e+03 pdb=" N4 C A 13 " -0.050 2.00e-02 2.50e+03 pdb=" C5 C A 13 " 0.019 2.00e-02 2.50e+03 pdb=" C6 C A 13 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 25 " -0.099 2.00e-02 2.50e+03 4.72e-02 5.02e+01 pdb=" N1 U A 25 " 0.060 2.00e-02 2.50e+03 pdb=" C2 U A 25 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U A 25 " 0.019 2.00e-02 2.50e+03 pdb=" N3 U A 25 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U A 25 " -0.030 2.00e-02 2.50e+03 pdb=" O4 U A 25 " -0.038 2.00e-02 2.50e+03 pdb=" C5 U A 25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 25 " 0.060 2.00e-02 2.50e+03 ... (remaining 3383 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 273 2.63 - 3.20: 17118 3.20 - 3.77: 32113 3.77 - 4.33: 46242 4.33 - 4.90: 74640 Nonbonded interactions: 170386 Sorted by model distance: nonbonded pdb=" OH TYR B 284 " pdb=" OE2 GLU B 348 " model vdw 2.067 3.040 nonbonded pdb="MG MG B 601 " pdb=" O3G ANP B 602 " model vdw 2.118 2.170 nonbonded pdb=" O GLY B 287 " pdb="MG MG B 601 " model vdw 2.183 2.170 nonbonded pdb=" OG SER C 258 " pdb=" O ARG C 267 " model vdw 2.227 3.040 nonbonded pdb=" OP2 U A 21 " pdb=" OG SER D 140 " model vdw 2.235 3.040 ... (remaining 170381 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 23.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 20510 Z= 0.640 Angle : 1.583 20.487 28123 Z= 1.015 Chirality : 0.088 0.772 3092 Planarity : 0.009 0.102 3386 Dihedral : 17.852 148.921 8202 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.77 % Rotamer: Outliers : 3.02 % Allowed : 7.52 % Favored : 89.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.39 % 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: 0.33 (0.16), residues: 2282 helix: 0.83 (0.19), residues: 641 sheet: 0.36 (0.25), residues: 376 loop : -0.05 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.005 ARG D 980 TYR 0.043 0.007 TYR D 786 PHE 0.042 0.007 PHE C 149 TRP 0.051 0.007 TRP D 362 HIS 0.018 0.004 HIS D 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.64 (20506) covalent geometry : angle 1.58249 / 1.02 (28117) hydrogen bonds : bond 0.18460 / 19.99 ( 804) hydrogen bonds : angle 6.70104 / 7.21 ( 2174) metal coordination : bond 0.07193 / 7.08 ( 4) metal coordination : angle 3.95975 / 7.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2910 (mmt) cc_final: 0.2687 (mtt) REVERT: B 4 TYR cc_start: 0.6349 (m-10) cc_final: 0.5475 (m-10) REVERT: B 8 GLU cc_start: 0.7001 (tt0) cc_final: 0.6367 (tp30) REVERT: B 139 ILE cc_start: 0.7383 (mt) cc_final: 0.7145 (mt) REVERT: B 164 ARG cc_start: 0.5700 (ttt90) cc_final: 0.5379 (ttp80) REVERT: B 199 LYS cc_start: 0.7408 (tptp) cc_final: 0.6878 (ttmm) REVERT: B 293 LYS cc_start: 0.7025 (mmtp) cc_final: 0.6409 (mmmt) REVERT: B 294 GLN cc_start: 0.7258 (mt0) cc_final: 0.6863 (mt0) REVERT: B 315 LYS cc_start: 0.6035 (mtmt) cc_final: 0.5663 (mttm) REVERT: B 326 LYS cc_start: 0.6566 (pttp) cc_final: 0.6269 (pttp) REVERT: B 340 GLU cc_start: 0.6856 (tp30) cc_final: 0.6536 (tp30) REVERT: B 470 MET cc_start: 0.7585 (mtp) cc_final: 0.7376 (mtp) REVERT: B 482 GLN cc_start: 0.6742 (pt0) cc_final: 0.6478 (pp30) REVERT: B 510 LYS cc_start: 0.6656 (pttm) cc_final: 0.6171 (mtpp) REVERT: B 525 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6223 (ttmt) REVERT: B 527 GLU cc_start: 0.7007 (pt0) cc_final: 0.6265 (mm-30) REVERT: B 529 ASP cc_start: 0.6885 (m-30) cc_final: 0.6608 (m-30) REVERT: C 22 ASP cc_start: 0.7104 (m-30) cc_final: 0.6849 (p0) REVERT: C 106 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5987 (pm20) REVERT: C 125 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7371 (mp0) REVERT: C 213 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7061 (p) REVERT: C 215 TYR cc_start: 0.7829 (p90) cc_final: 0.7336 (p90) REVERT: C 224 TYR cc_start: 0.7265 (m-80) cc_final: 0.6965 (m-80) REVERT: C 257 TRP cc_start: 0.6516 (t60) cc_final: 0.6285 (t60) REVERT: C 321 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7495 (ttm110) REVERT: C 344 ASP cc_start: 0.7503 (m-30) cc_final: 0.7243 (m-30) REVERT: C 367 GLU cc_start: 0.8196 (pt0) cc_final: 0.7889 (pt0) REVERT: C 379 HIS cc_start: 0.8013 (m-70) cc_final: 0.7693 (m170) REVERT: C 440 GLU cc_start: 0.6594 (tt0) cc_final: 0.6318 (mt-10) REVERT: C 442 GLU cc_start: 0.6864 (tt0) cc_final: 0.6331 (tm-30) REVERT: C 500 GLU cc_start: 0.7205 (tt0) cc_final: 0.6806 (tt0) REVERT: C 525 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6807 (mt-10) REVERT: C 575 GLU cc_start: 0.7284 (tt0) cc_final: 0.6479 (pt0) REVERT: C 583 GLU cc_start: 0.6662 (pt0) cc_final: 0.6353 (pm20) REVERT: C 608 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5812 (mp0) REVERT: C 624 THR cc_start: 0.6897 (m) cc_final: 0.6639 (p) REVERT: D 35 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 38 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7027 (mm-30) REVERT: D 42 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.5674 (p0) REVERT: D 90 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5887 (mt-10) REVERT: D 102 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6176 (mm-30) REVERT: D 178 LYS cc_start: 0.7110 (tttm) cc_final: 0.6849 (mmpt) REVERT: D 179 ASP cc_start: 0.7292 (m-30) cc_final: 0.6937 (m-30) REVERT: D 234 SER cc_start: 0.7530 (p) cc_final: 0.7183 (m) REVERT: D 237 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5357 (ptp-170) REVERT: D 296 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4771 (p0) REVERT: D 297 GLN cc_start: 0.4221 (OUTLIER) cc_final: 0.3845 (pm20) REVERT: D 376 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7751 (tp30) REVERT: D 412 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7899 (mmmt) REVERT: D 418 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: D 529 LYS cc_start: 0.6805 (mmtp) cc_final: 0.6381 (mptp) REVERT: D 649 ARG cc_start: 0.7108 (ptp-170) cc_final: 0.6760 (ptm160) REVERT: D 714 VAL cc_start: 0.6328 (OUTLIER) cc_final: 0.6099 (t) REVERT: D 716 GLN cc_start: 0.1696 (OUTLIER) cc_final: 0.1432 (mp10) REVERT: D 883 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7311 (mmpt) REVERT: D 961 ASP cc_start: 0.6885 (m-30) cc_final: 0.6268 (OUTLIER) REVERT: D 993 ASP cc_start: 0.7525 (m-30) cc_final: 0.7089 (m-30) REVERT: D 1020 GLU cc_start: 0.7547 (tt0) cc_final: 0.7343 (tp30) REVERT: D 1087 GLN cc_start: 0.7294 (mt0) cc_final: 0.6780 (mp10) REVERT: D 1145 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6109 (pt0) REVERT: D 1230 GLU cc_start: 0.7068 (tt0) cc_final: 0.6734 (tp30) outliers start: 59 outliers final: 19 residues processed: 373 average time/residue: 0.6333 time to fit residues: 265.2183 Evaluate side-chains 247 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1178 ARG Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0030 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN B 205 ASN B 495 GLN B 496 GLN B 524 GLN C 36 GLN C 40 HIS C 139 ASN C 288 HIS C 385 GLN C 391 GLN C 531 HIS D 50 GLN D 310 ASN D 421 ASN D 693 GLN D 716 GLN ** D 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN D1153 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.171572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138415 restraints weight = 21690.356| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.24 r_work: 0.3246 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20510 Z= 0.142 Angle : 0.627 9.850 28123 Z= 0.343 Chirality : 0.045 0.235 3092 Planarity : 0.004 0.038 3386 Dihedral : 16.080 154.964 3782 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.02 % Allowed : 11.66 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 2282 helix: 1.58 (0.20), residues: 635 sheet: 0.49 (0.24), residues: 392 loop : 0.50 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 988 TYR 0.019 0.002 TYR B 153 PHE 0.017 0.002 PHE D 401 TRP 0.012 0.001 TRP D 859 HIS 0.006 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (20506) covalent geometry : angle 0.62572 / 0.34 (28117) hydrogen bonds : bond 0.05732 / 6.05 ( 804) hydrogen bonds : angle 5.04306 / 5.58 ( 2174) metal coordination : bond 0.00171 / 0.15 ( 4) metal coordination : angle 2.56877 / 5.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.6826 (m-10) cc_final: 0.6068 (m-10) REVERT: B 34 GLU cc_start: 0.6327 (mm-30) cc_final: 0.6115 (mm-30) REVERT: B 36 MET cc_start: 0.6768 (tpp) cc_final: 0.5978 (tpp) REVERT: B 164 ARG cc_start: 0.5842 (ttt90) cc_final: 0.5611 (ttp80) REVERT: B 245 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.5789 (t80) REVERT: B 293 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7485 (mmmt) REVERT: B 315 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6957 (mttm) REVERT: B 323 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 327 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5502 (pm20) REVERT: B 332 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6684 (mmm-85) REVERT: B 348 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 388 ARG cc_start: 0.6422 (mmp80) cc_final: 0.6191 (mmp80) REVERT: B 504 GLU cc_start: 0.7850 (mp0) cc_final: 0.7601 (mp0) REVERT: B 507 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7531 (mtmt) REVERT: B 525 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6857 (ttmt) REVERT: B 527 GLU cc_start: 0.7879 (pt0) cc_final: 0.7361 (mm-30) REVERT: B 529 ASP cc_start: 0.7783 (m-30) cc_final: 0.7452 (m-30) REVERT: C 106 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6577 (pm20) REVERT: C 125 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8274 (mp0) REVERT: C 213 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7248 (p) REVERT: C 224 TYR cc_start: 0.7956 (m-80) cc_final: 0.7375 (m-80) REVERT: C 321 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7975 (ttm110) REVERT: C 367 GLU cc_start: 0.8553 (pt0) cc_final: 0.8328 (pt0) REVERT: C 422 ARG cc_start: 0.6409 (ttp80) cc_final: 0.6177 (ttp80) REVERT: C 440 GLU cc_start: 0.7134 (tt0) cc_final: 0.6844 (pt0) REVERT: C 442 GLU cc_start: 0.7146 (tt0) cc_final: 0.6841 (tm-30) REVERT: C 454 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: C 507 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7336 (ttp80) REVERT: C 575 GLU cc_start: 0.7635 (tt0) cc_final: 0.6953 (pt0) REVERT: C 608 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: C 623 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6868 (mp) REVERT: D 26 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: D 35 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8468 (mm-30) REVERT: D 100 ASP cc_start: 0.7969 (t0) cc_final: 0.7698 (m-30) REVERT: D 166 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7299 (mtp180) REVERT: D 237 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6285 (ptp-110) REVERT: D 513 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 541 LYS cc_start: 0.8007 (mttp) cc_final: 0.7555 (mtmt) REVERT: D 649 ARG cc_start: 0.7672 (ptp-170) cc_final: 0.7116 (ptm160) REVERT: D 739 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7822 (tmtm) REVERT: D 883 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8431 (mmpt) REVERT: D 961 ASP cc_start: 0.7084 (m-30) cc_final: 0.6754 (OUTLIER) REVERT: D 1145 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6864 (pt0) REVERT: D 1178 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8845 (ptp-170) outliers start: 59 outliers final: 17 residues processed: 301 average time/residue: 0.6585 time to fit residues: 221.6845 Evaluate side-chains 243 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1178 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 91 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 chunk 50 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN C 2 GLN C 36 GLN C 296 ASN C 379 HIS D 285 ASN D 421 ASN D 588 ASN D 699 HIS D 747 HIS D 763 ASN D 818 HIS D1153 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140073 restraints weight = 21845.579| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.21 r_work: 0.3241 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20510 Z= 0.164 Angle : 0.612 7.138 28123 Z= 0.331 Chirality : 0.046 0.228 3092 Planarity : 0.005 0.039 3386 Dihedral : 15.394 156.803 3748 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.63 % Allowed : 12.94 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 2282 helix: 1.65 (0.20), residues: 643 sheet: 0.52 (0.25), residues: 390 loop : 0.44 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 988 TYR 0.014 0.002 TYR B 282 PHE 0.029 0.002 PHE B 438 TRP 0.014 0.001 TRP D 695 HIS 0.007 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (20506) covalent geometry : angle 0.61053 / 0.33 (28117) hydrogen bonds : bond 0.05632 / 5.93 ( 804) hydrogen bonds : angle 4.85620 / 5.34 ( 2174) metal coordination : bond 0.00430 / 0.37 ( 4) metal coordination : angle 2.76304 / 5.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.6873 (m-10) cc_final: 0.6524 (m-10) REVERT: B 18 ASP cc_start: 0.8015 (p0) cc_final: 0.7774 (p0) REVERT: B 34 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.6060 (mm-30) REVERT: B 140 LYS cc_start: 0.7046 (ttpp) cc_final: 0.6483 (ttmm) REVERT: B 172 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6911 (mmt90) REVERT: B 245 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5787 (t80) REVERT: B 293 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7460 (mmmt) REVERT: B 315 LYS cc_start: 0.7354 (mtmt) cc_final: 0.6878 (mttm) REVERT: B 340 GLU cc_start: 0.7487 (tp30) cc_final: 0.7209 (tp30) REVERT: B 388 ARG cc_start: 0.6542 (mmp80) cc_final: 0.6299 (mmp80) REVERT: B 399 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7808 (mppt) REVERT: B 525 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6950 (ttmm) REVERT: B 527 GLU cc_start: 0.7805 (pt0) cc_final: 0.7399 (mm-30) REVERT: B 529 ASP cc_start: 0.8010 (m-30) cc_final: 0.7668 (m-30) REVERT: C 106 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6571 (pm20) REVERT: C 112 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6144 (ttp80) REVERT: C 125 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8323 (mp0) REVERT: C 224 TYR cc_start: 0.8130 (m-80) cc_final: 0.7871 (m-80) REVERT: C 321 ARG cc_start: 0.8355 (mtp180) cc_final: 0.8082 (ttm110) REVERT: C 367 GLU cc_start: 0.8629 (pt0) cc_final: 0.8395 (pt0) REVERT: C 422 ARG cc_start: 0.6654 (ttp80) cc_final: 0.6422 (ttp80) REVERT: C 442 GLU cc_start: 0.7312 (tt0) cc_final: 0.6896 (tm-30) REVERT: C 454 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: C 554 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6066 (p0) REVERT: C 567 GLN cc_start: 0.7827 (mm110) cc_final: 0.7522 (mm-40) REVERT: C 575 GLU cc_start: 0.7683 (tt0) cc_final: 0.6999 (pt0) REVERT: C 583 GLU cc_start: 0.7088 (pm20) cc_final: 0.6285 (mp0) REVERT: C 608 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6083 (mp0) REVERT: C 623 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6817 (mp) REVERT: D 20 ILE cc_start: 0.8273 (mt) cc_final: 0.8011 (mp) REVERT: D 26 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: D 35 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8403 (mm-30) REVERT: D 48 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7532 (mmt180) REVERT: D 100 ASP cc_start: 0.7987 (t0) cc_final: 0.7751 (m-30) REVERT: D 210 MET cc_start: 0.9133 (mmm) cc_final: 0.8896 (tpp) REVERT: D 237 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6476 (ptp-110) REVERT: D 513 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8146 (p) REVERT: D 529 LYS cc_start: 0.7384 (mptp) cc_final: 0.7173 (mptp) REVERT: D 541 LYS cc_start: 0.8214 (mttp) cc_final: 0.7734 (mtmt) REVERT: D 561 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6753 (p0) REVERT: D 670 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7135 (mm) REVERT: D 883 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8478 (mmpt) REVERT: D 961 ASP cc_start: 0.7091 (m-30) cc_final: 0.6808 (OUTLIER) REVERT: D 972 LYS cc_start: 0.8556 (pttt) cc_final: 0.8284 (pttm) REVERT: D 1145 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6926 (pt0) REVERT: D 1160 GLU cc_start: 0.7585 (tp30) cc_final: 0.7095 (mp0) outliers start: 71 outliers final: 25 residues processed: 287 average time/residue: 0.6445 time to fit residues: 206.7884 Evaluate side-chains 259 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1195 SER Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 218 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 220 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 109 optimal weight: 0.3980 chunk 5 optimal weight: 8.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN C 36 GLN D 421 ASN D 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.173769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141649 restraints weight = 21936.889| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.15 r_work: 0.3283 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20510 Z= 0.099 Angle : 0.509 6.976 28123 Z= 0.279 Chirality : 0.042 0.214 3092 Planarity : 0.004 0.039 3386 Dihedral : 15.236 164.331 3740 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.61 % Allowed : 14.58 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 1.32 (0.17), residues: 2282 helix: 1.96 (0.20), residues: 638 sheet: 0.62 (0.25), residues: 386 loop : 0.51 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 988 TYR 0.010 0.001 TYR B 282 PHE 0.026 0.001 PHE B 438 TRP 0.013 0.001 TRP D 429 HIS 0.004 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (20506) covalent geometry : angle 0.50804 / 0.28 (28117) hydrogen bonds : bond 0.04488 / 4.69 ( 804) hydrogen bonds : angle 4.58845 / 5.05 ( 2174) metal coordination : bond 0.00222 / 0.20 ( 4) metal coordination : angle 2.40429 / 4.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.6875 (m-10) cc_final: 0.6594 (m-10) REVERT: B 293 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7471 (mmmt) REVERT: B 332 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6751 (mmm-85) REVERT: B 340 GLU cc_start: 0.7481 (tp30) cc_final: 0.7178 (tp30) REVERT: B 348 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 388 ARG cc_start: 0.6466 (mmp80) cc_final: 0.6178 (mmp80) REVERT: B 504 GLU cc_start: 0.8031 (mp0) cc_final: 0.7074 (mm-30) REVERT: B 525 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6882 (ttmm) REVERT: B 527 GLU cc_start: 0.7830 (pt0) cc_final: 0.7357 (mm-30) REVERT: B 529 ASP cc_start: 0.7881 (m-30) cc_final: 0.7540 (m-30) REVERT: C 106 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6513 (pm20) REVERT: C 125 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8301 (mp0) REVERT: C 224 TYR cc_start: 0.8073 (m-80) cc_final: 0.7750 (m-80) REVERT: C 340 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8243 (tmtp) REVERT: C 367 GLU cc_start: 0.8540 (pt0) cc_final: 0.8302 (pt0) REVERT: C 422 ARG cc_start: 0.6539 (ttp80) cc_final: 0.6325 (ttp80) REVERT: C 454 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: C 555 MET cc_start: 0.7772 (tpp) cc_final: 0.7449 (tpt) REVERT: C 567 GLN cc_start: 0.7825 (mm110) cc_final: 0.7562 (mm-40) REVERT: C 575 GLU cc_start: 0.7626 (tt0) cc_final: 0.6916 (pt0) REVERT: C 583 GLU cc_start: 0.6978 (pm20) cc_final: 0.6375 (mp0) REVERT: C 608 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6013 (mp0) REVERT: D 20 ILE cc_start: 0.8266 (mt) cc_final: 0.8025 (mp) REVERT: D 26 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: D 48 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7368 (mmt180) REVERT: D 100 ASP cc_start: 0.7914 (t0) cc_final: 0.7673 (m-30) REVERT: D 194 THR cc_start: 0.8553 (p) cc_final: 0.8316 (p) REVERT: D 210 MET cc_start: 0.9105 (mmm) cc_final: 0.8869 (tpp) REVERT: D 237 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6385 (ptp-110) REVERT: D 461 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7743 (tp30) REVERT: D 513 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8069 (p) REVERT: D 541 LYS cc_start: 0.8193 (mttp) cc_final: 0.7818 (mtmt) REVERT: D 685 MET cc_start: 0.6294 (tpp) cc_final: 0.5988 (tpt) REVERT: D 784 GLU cc_start: 0.7588 (pt0) cc_final: 0.7382 (pt0) REVERT: D 883 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8466 (mmpt) REVERT: D 961 ASP cc_start: 0.7003 (m-30) cc_final: 0.6803 (OUTLIER) REVERT: D 1082 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: D 1160 GLU cc_start: 0.7505 (tp30) cc_final: 0.6794 (tp30) outliers start: 51 outliers final: 22 residues processed: 268 average time/residue: 0.6523 time to fit residues: 196.2227 Evaluate side-chains 238 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 200 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN B 495 GLN B 537 HIS C 36 GLN D 588 ASN D1145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.173396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142480 restraints weight = 21771.980| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.05 r_work: 0.3286 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20510 Z= 0.119 Angle : 0.527 7.812 28123 Z= 0.286 Chirality : 0.043 0.221 3092 Planarity : 0.004 0.040 3386 Dihedral : 15.001 164.357 3740 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.56 % Allowed : 14.99 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 1.29 (0.17), residues: 2282 helix: 1.95 (0.20), residues: 644 sheet: 0.59 (0.25), residues: 389 loop : 0.47 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 988 TYR 0.012 0.001 TYR B 282 PHE 0.030 0.002 PHE B 438 TRP 0.014 0.001 TRP D 429 HIS 0.005 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (20506) covalent geometry : angle 0.52604 / 0.29 (28117) hydrogen bonds : bond 0.04636 / 4.86 ( 804) hydrogen bonds : angle 4.56748 / 5.04 ( 2174) metal coordination : bond 0.00234 / 0.20 ( 4) metal coordination : angle 2.38400 / 4.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.6979 (m-10) cc_final: 0.6680 (m-10) REVERT: B 18 ASP cc_start: 0.7951 (p0) cc_final: 0.7708 (p0) REVERT: B 293 LYS cc_start: 0.7739 (mmtp) cc_final: 0.7435 (mmmt) REVERT: B 327 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5744 (pm20) REVERT: B 340 GLU cc_start: 0.7451 (tp30) cc_final: 0.7166 (tp30) REVERT: B 399 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7741 (mppt) REVERT: B 504 GLU cc_start: 0.8094 (mp0) cc_final: 0.7088 (mm-30) REVERT: B 507 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7637 (mttt) REVERT: B 525 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6874 (ttmm) REVERT: B 527 GLU cc_start: 0.7725 (pt0) cc_final: 0.7403 (mm-30) REVERT: B 529 ASP cc_start: 0.7842 (m-30) cc_final: 0.7503 (m-30) REVERT: C 106 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6617 (pm20) REVERT: C 125 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8294 (mp0) REVERT: C 220 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7658 (mp) REVERT: C 224 TYR cc_start: 0.8073 (m-80) cc_final: 0.7852 (m-80) REVERT: C 340 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (tmtp) REVERT: C 422 ARG cc_start: 0.6567 (ttp80) cc_final: 0.6336 (ttp80) REVERT: C 454 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: C 555 MET cc_start: 0.7797 (tpp) cc_final: 0.7485 (tpt) REVERT: C 567 GLN cc_start: 0.7803 (mm110) cc_final: 0.7566 (mm-40) REVERT: C 575 GLU cc_start: 0.7598 (tt0) cc_final: 0.6971 (pt0) REVERT: C 583 GLU cc_start: 0.6964 (pm20) cc_final: 0.6365 (mp0) REVERT: C 608 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: D 20 ILE cc_start: 0.8265 (mt) cc_final: 0.8016 (mp) REVERT: D 26 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: D 100 ASP cc_start: 0.7944 (t0) cc_final: 0.7728 (m-30) REVERT: D 166 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7435 (mtp180) REVERT: D 194 THR cc_start: 0.8597 (p) cc_final: 0.8344 (p) REVERT: D 237 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6293 (ptp-170) REVERT: D 244 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5180 (ttpp) REVERT: D 513 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8086 (p) REVERT: D 541 LYS cc_start: 0.8252 (mttp) cc_final: 0.7876 (mtmt) REVERT: D 685 MET cc_start: 0.6403 (tpp) cc_final: 0.6154 (tpt) REVERT: D 883 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8470 (mmpt) REVERT: D 1082 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: D 1160 GLU cc_start: 0.7491 (tp30) cc_final: 0.6734 (tp30) REVERT: D 1184 GLN cc_start: 0.8904 (mt0) cc_final: 0.8679 (mt0) outliers start: 50 outliers final: 25 residues processed: 253 average time/residue: 0.6213 time to fit residues: 176.0975 Evaluate side-chains 244 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 961 ASP Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN C 36 GLN D 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.172406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140797 restraints weight = 21681.342| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.13 r_work: 0.3255 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20510 Z= 0.133 Angle : 0.534 7.955 28123 Z= 0.290 Chirality : 0.043 0.215 3092 Planarity : 0.004 0.040 3386 Dihedral : 14.922 163.188 3740 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.51 % Allowed : 15.35 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 1.24 (0.17), residues: 2282 helix: 1.98 (0.20), residues: 638 sheet: 0.50 (0.25), residues: 390 loop : 0.43 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 988 TYR 0.012 0.001 TYR B 282 PHE 0.031 0.002 PHE B 438 TRP 0.015 0.001 TRP D 429 HIS 0.006 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (20506) covalent geometry : angle 0.53317 / 0.29 (28117) hydrogen bonds : bond 0.04707 / 4.94 ( 804) hydrogen bonds : angle 4.58858 / 5.05 ( 2174) metal coordination : bond 0.00193 / 0.17 ( 4) metal coordination : angle 2.36412 / 4.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.7013 (m-10) cc_final: 0.6775 (m-10) REVERT: B 18 ASP cc_start: 0.8125 (p0) cc_final: 0.7851 (p0) REVERT: B 245 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5548 (t80) REVERT: B 293 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7475 (mmmt) REVERT: B 340 GLU cc_start: 0.7515 (tp30) cc_final: 0.7157 (tp30) REVERT: B 399 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: B 504 GLU cc_start: 0.8156 (mp0) cc_final: 0.7141 (mm-30) REVERT: B 507 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7723 (mttt) REVERT: B 527 GLU cc_start: 0.7741 (pt0) cc_final: 0.7400 (mm-30) REVERT: B 529 ASP cc_start: 0.7892 (m-30) cc_final: 0.7548 (m-30) REVERT: C 106 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6618 (pm20) REVERT: C 125 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8333 (mp0) REVERT: C 220 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 340 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8267 (tmtp) REVERT: C 422 ARG cc_start: 0.6644 (ttp80) cc_final: 0.6367 (ttp80) REVERT: C 454 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6806 (mp10) REVERT: C 555 MET cc_start: 0.7789 (tpp) cc_final: 0.7482 (tpt) REVERT: C 567 GLN cc_start: 0.7807 (mm110) cc_final: 0.7558 (mm-40) REVERT: C 575 GLU cc_start: 0.7703 (tt0) cc_final: 0.7036 (pt0) REVERT: C 583 GLU cc_start: 0.7120 (pm20) cc_final: 0.6496 (mp0) REVERT: C 608 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: D 20 ILE cc_start: 0.8268 (mt) cc_final: 0.8037 (mp) REVERT: D 26 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: D 166 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7429 (mtp180) REVERT: D 194 THR cc_start: 0.8572 (p) cc_final: 0.8340 (p) REVERT: D 237 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6179 (ptp90) REVERT: D 244 LYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5183 (ttpp) REVERT: D 461 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7869 (tp30) REVERT: D 513 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (p) REVERT: D 541 LYS cc_start: 0.8370 (mttp) cc_final: 0.7980 (mtmt) REVERT: D 685 MET cc_start: 0.6586 (tpp) cc_final: 0.6365 (tpt) REVERT: D 883 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8447 (mmpt) REVERT: D 1082 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: D 1160 GLU cc_start: 0.7572 (tp30) cc_final: 0.6806 (tp30) outliers start: 49 outliers final: 26 residues processed: 246 average time/residue: 0.6523 time to fit residues: 179.8052 Evaluate side-chains 244 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 865 ASP Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN B 537 HIS C 36 GLN D 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138673 restraints weight = 21687.645| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.15 r_work: 0.3227 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20510 Z= 0.183 Angle : 0.588 7.667 28123 Z= 0.316 Chirality : 0.046 0.222 3092 Planarity : 0.005 0.040 3386 Dihedral : 14.848 158.834 3734 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.76 % Allowed : 15.40 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 2282 helix: 1.81 (0.20), residues: 638 sheet: 0.37 (0.25), residues: 399 loop : 0.32 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 133 TYR 0.014 0.002 TYR B 282 PHE 0.031 0.002 PHE B 438 TRP 0.016 0.002 TRP C 589 HIS 0.008 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (20506) covalent geometry : angle 0.58643 / 0.32 (28117) hydrogen bonds : bond 0.05239 / 5.51 ( 804) hydrogen bonds : angle 4.69982 / 5.15 ( 2174) metal coordination : bond 0.00348 / 0.32 ( 4) metal coordination : angle 2.69148 / 5.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.7068 (m-10) cc_final: 0.6770 (m-10) REVERT: B 245 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.5864 (t80) REVERT: B 293 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7498 (mmmt) REVERT: B 295 LYS cc_start: 0.6967 (tttp) cc_final: 0.6743 (ttmt) REVERT: B 340 GLU cc_start: 0.7551 (tp30) cc_final: 0.7203 (tp30) REVERT: B 399 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7835 (mppt) REVERT: B 527 GLU cc_start: 0.7775 (pt0) cc_final: 0.7431 (mm-30) REVERT: B 529 ASP cc_start: 0.7869 (m-30) cc_final: 0.7547 (m-30) REVERT: C 106 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6610 (pm20) REVERT: C 112 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.5928 (ttp80) REVERT: C 125 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8320 (mp0) REVERT: C 340 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8284 (tmtp) REVERT: C 422 ARG cc_start: 0.6710 (ttp80) cc_final: 0.6422 (ttp80) REVERT: C 454 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: C 507 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7814 (ttp-110) REVERT: C 555 MET cc_start: 0.7789 (tpp) cc_final: 0.7497 (tpt) REVERT: C 567 GLN cc_start: 0.7795 (mm110) cc_final: 0.7553 (mm-40) REVERT: C 575 GLU cc_start: 0.7760 (tt0) cc_final: 0.7029 (pt0) REVERT: C 583 GLU cc_start: 0.7006 (pm20) cc_final: 0.6383 (mp0) REVERT: C 608 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: D 20 ILE cc_start: 0.8267 (mt) cc_final: 0.8025 (mp) REVERT: D 26 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: D 166 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7427 (mtp180) REVERT: D 237 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6160 (ptp90) REVERT: D 244 LYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5201 (ttpp) REVERT: D 513 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8085 (p) REVERT: D 541 LYS cc_start: 0.8447 (mttp) cc_final: 0.7923 (mtmt) REVERT: D 685 MET cc_start: 0.6647 (tpp) cc_final: 0.6441 (tpt) REVERT: D 740 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7418 (m-40) REVERT: D 866 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8754 (mttt) REVERT: D 883 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8463 (mmpt) REVERT: D 1082 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7752 (mt-10) outliers start: 54 outliers final: 27 residues processed: 243 average time/residue: 0.6554 time to fit residues: 177.9059 Evaluate side-chains 242 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 866 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 117 optimal weight: 0.0980 chunk 161 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN B 537 HIS C 36 GLN D 223 HIS D 540 HIS D 588 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.169299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137943 restraints weight = 21680.020| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.13 r_work: 0.3218 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20510 Z= 0.182 Angle : 0.598 7.289 28123 Z= 0.322 Chirality : 0.046 0.222 3092 Planarity : 0.005 0.041 3386 Dihedral : 14.844 156.368 3734 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.66 % Allowed : 15.60 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.86 (0.17), residues: 2282 helix: 1.67 (0.20), residues: 638 sheet: 0.27 (0.25), residues: 405 loop : 0.19 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 988 TYR 0.014 0.002 TYR B 282 PHE 0.031 0.002 PHE B 438 TRP 0.020 0.002 TRP C 589 HIS 0.007 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (20506) covalent geometry : angle 0.59718 / 0.32 (28117) hydrogen bonds : bond 0.05358 / 5.63 ( 804) hydrogen bonds : angle 4.77253 / 5.24 ( 2174) metal coordination : bond 0.00338 / 0.31 ( 4) metal coordination : angle 2.64493 / 5.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.7124 (m-10) cc_final: 0.6895 (m-10) REVERT: B 293 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7484 (mmmt) REVERT: B 295 LYS cc_start: 0.7041 (tttp) cc_final: 0.6725 (ttmt) REVERT: B 340 GLU cc_start: 0.7554 (tp30) cc_final: 0.7255 (tp30) REVERT: B 399 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7898 (mppt) REVERT: B 527 GLU cc_start: 0.7809 (pt0) cc_final: 0.7417 (mm-30) REVERT: B 529 ASP cc_start: 0.7834 (m-30) cc_final: 0.7499 (m-30) REVERT: C 74 PHE cc_start: 0.6488 (t80) cc_final: 0.6176 (t80) REVERT: C 106 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6614 (pm20) REVERT: C 112 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6012 (ttp80) REVERT: C 125 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8310 (mp0) REVERT: C 340 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8262 (tmtp) REVERT: C 422 ARG cc_start: 0.6812 (ttp80) cc_final: 0.6374 (ttp80) REVERT: C 454 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: C 507 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7873 (ttp-110) REVERT: C 555 MET cc_start: 0.7748 (tpp) cc_final: 0.7471 (tpt) REVERT: C 567 GLN cc_start: 0.7838 (mm110) cc_final: 0.7573 (mm-40) REVERT: C 583 GLU cc_start: 0.6944 (pm20) cc_final: 0.6357 (mp0) REVERT: D 20 ILE cc_start: 0.8245 (mt) cc_final: 0.8004 (mp) REVERT: D 26 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: D 166 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: D 237 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6145 (ptp90) REVERT: D 244 LYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5220 (ttpp) REVERT: D 513 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8118 (p) REVERT: D 541 LYS cc_start: 0.8434 (mttp) cc_final: 0.7989 (mtmt) REVERT: D 685 MET cc_start: 0.6655 (tpp) cc_final: 0.6405 (tpt) REVERT: D 740 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: D 866 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8710 (mttp) REVERT: D 883 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8466 (mmpt) REVERT: D 1082 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 1160 GLU cc_start: 0.7782 (tp30) cc_final: 0.6832 (mm-30) outliers start: 52 outliers final: 26 residues processed: 244 average time/residue: 0.6273 time to fit residues: 170.9710 Evaluate side-chains 243 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 865 ASP Chi-restraints excluded: chain D residue 866 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN B 537 HIS C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.171052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139893 restraints weight = 21559.836| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.10 r_work: 0.3247 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20510 Z= 0.128 Angle : 0.683 42.989 28123 Z= 0.344 Chirality : 0.043 0.213 3092 Planarity : 0.004 0.042 3386 Dihedral : 14.852 159.723 3734 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.20 % Allowed : 16.11 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.96 (0.17), residues: 2282 helix: 1.82 (0.20), residues: 638 sheet: 0.29 (0.25), residues: 405 loop : 0.23 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 988 TYR 0.013 0.001 TYR C 224 PHE 0.030 0.002 PHE B 438 TRP 0.020 0.001 TRP C 589 HIS 0.005 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (20506) covalent geometry : angle 0.68202 / 0.34 (28117) hydrogen bonds : bond 0.04835 / 5.05 ( 804) hydrogen bonds : angle 4.65934 / 5.11 ( 2174) metal coordination : bond 0.00197 / 0.18 ( 4) metal coordination : angle 2.11084 / 4.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.7103 (m-10) cc_final: 0.6850 (m-10) REVERT: B 263 ASP cc_start: 0.8027 (p0) cc_final: 0.7744 (p0) REVERT: B 293 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7449 (mmmt) REVERT: B 295 LYS cc_start: 0.7003 (tttp) cc_final: 0.6734 (ttmt) REVERT: B 340 GLU cc_start: 0.7485 (tp30) cc_final: 0.7219 (tp30) REVERT: B 399 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7867 (mppt) REVERT: B 527 GLU cc_start: 0.7776 (pt0) cc_final: 0.7458 (mm-30) REVERT: B 529 ASP cc_start: 0.7810 (m-30) cc_final: 0.7473 (m-30) REVERT: C 106 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6606 (pm20) REVERT: C 112 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.5882 (ttp80) REVERT: C 125 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8303 (mp0) REVERT: C 340 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8273 (tmtp) REVERT: C 422 ARG cc_start: 0.6734 (ttp80) cc_final: 0.6338 (ttp80) REVERT: C 454 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: C 507 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7905 (ttp-110) REVERT: C 555 MET cc_start: 0.7733 (tpp) cc_final: 0.7460 (tpt) REVERT: C 567 GLN cc_start: 0.7833 (mm110) cc_final: 0.7557 (mm-40) REVERT: C 583 GLU cc_start: 0.6886 (pm20) cc_final: 0.6272 (mp0) REVERT: C 608 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: D 20 ILE cc_start: 0.8260 (mt) cc_final: 0.8019 (mp) REVERT: D 26 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: D 166 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7421 (mtp180) REVERT: D 237 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6121 (ptp90) REVERT: D 244 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5225 (ttpp) REVERT: D 283 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.8945 (pt) REVERT: D 513 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (p) REVERT: D 541 LYS cc_start: 0.8435 (mttp) cc_final: 0.7983 (mtmt) REVERT: D 685 MET cc_start: 0.6696 (tpp) cc_final: 0.6477 (tpt) REVERT: D 866 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8753 (mttt) REVERT: D 883 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8465 (mmpt) REVERT: D 1082 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: D 1160 GLU cc_start: 0.7624 (tp30) cc_final: 0.6730 (mm-30) outliers start: 43 outliers final: 21 residues processed: 242 average time/residue: 0.6767 time to fit residues: 182.9044 Evaluate side-chains 239 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 866 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 186 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 202 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 309 GLN B 537 HIS C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138459 restraints weight = 21708.398| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.09 r_work: 0.3210 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20510 Z= 0.177 Angle : 0.592 7.004 28123 Z= 0.319 Chirality : 0.046 0.220 3092 Planarity : 0.005 0.041 3386 Dihedral : 14.802 157.872 3734 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.94 % Allowed : 16.32 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.85 (0.17), residues: 2282 helix: 1.71 (0.20), residues: 638 sheet: 0.21 (0.24), residues: 405 loop : 0.17 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 988 TYR 0.015 0.002 TYR C 224 PHE 0.031 0.002 PHE B 438 TRP 0.026 0.002 TRP C 589 HIS 0.008 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (20506) covalent geometry : angle 0.59091 / 0.32 (28117) hydrogen bonds : bond 0.05313 / 5.58 ( 804) hydrogen bonds : angle 4.76263 / 5.22 ( 2174) metal coordination : bond 0.00306 / 0.28 ( 4) metal coordination : angle 2.61870 / 5.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4564 Ramachandran restraints generated. 2282 Oldfield, 0 Emsley, 2282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 TYR cc_start: 0.7150 (m-10) cc_final: 0.6887 (m-10) REVERT: B 293 LYS cc_start: 0.7786 (mmtp) cc_final: 0.7502 (mmmt) REVERT: B 340 GLU cc_start: 0.7618 (tp30) cc_final: 0.7342 (tp30) REVERT: B 399 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7904 (mppt) REVERT: B 527 GLU cc_start: 0.7813 (pt0) cc_final: 0.7427 (mm-30) REVERT: B 529 ASP cc_start: 0.7852 (m-30) cc_final: 0.7523 (m-30) REVERT: C 36 GLN cc_start: 0.7037 (mt0) cc_final: 0.6468 (pt0) REVERT: C 106 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6596 (pm20) REVERT: C 112 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6026 (ttp80) REVERT: C 125 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8319 (mp0) REVERT: C 275 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7401 (tppt) REVERT: C 340 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8266 (tmtp) REVERT: C 422 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6384 (ttp80) REVERT: C 454 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: C 507 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7935 (ttp-110) REVERT: C 555 MET cc_start: 0.7768 (tpp) cc_final: 0.7499 (tpt) REVERT: C 567 GLN cc_start: 0.7859 (mm110) cc_final: 0.7537 (mm-40) REVERT: D 20 ILE cc_start: 0.8250 (mt) cc_final: 0.8007 (mp) REVERT: D 26 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: D 166 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7433 (mtp180) REVERT: D 237 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6299 (ptp90) REVERT: D 244 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5234 (ttpp) REVERT: D 513 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8102 (p) REVERT: D 541 LYS cc_start: 0.8466 (mttp) cc_final: 0.7988 (mtmt) REVERT: D 685 MET cc_start: 0.6753 (tpp) cc_final: 0.6532 (tpt) REVERT: D 883 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8462 (mmpt) REVERT: D 1082 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: D 1160 GLU cc_start: 0.7744 (tp30) cc_final: 0.6808 (mm-30) outliers start: 38 outliers final: 23 residues processed: 232 average time/residue: 0.7036 time to fit residues: 182.7788 Evaluate side-chains 235 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1085 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 117 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN B 537 HIS C 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.165698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133612 restraints weight = 21619.768| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.18 r_work: 0.3156 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20510 Z= 0.139 Angle : 0.550 6.832 28123 Z= 0.299 Chirality : 0.044 0.214 3092 Planarity : 0.004 0.041 3386 Dihedral : 14.809 160.087 3734 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.89 % Allowed : 16.78 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.93 (0.17), residues: 2282 helix: 1.78 (0.20), residues: 638 sheet: 0.35 (0.25), residues: 395 loop : 0.18 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 988 TYR 0.013 0.001 TYR C 215 PHE 0.030 0.002 PHE B 438 TRP 0.028 0.001 TRP C 589 HIS 0.006 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (20506) covalent geometry : angle 0.54874 / 0.30 (28117) hydrogen bonds : bond 0.04884 / 5.11 ( 804) hydrogen bonds : angle 4.68025 / 5.14 ( 2174) metal coordination : bond 0.00203 / 0.18 ( 4) metal coordination : angle 2.17004 / 4.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5967.45 seconds wall clock time: 102 minutes 37.05 seconds (6157.05 seconds total)