Starting phenix.real_space_refine on Fri Aug 7 09:27:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wxh_66346/08_2026/9wxh_66346.map" } resolution = 2.6 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= 0.030 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 80 5.49 5 Mg 4 5.21 5 S 63 5.16 5 C 12358 2.51 5 N 3538 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20118 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 841 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 19, 'rna3p': 20} Chain: "B" Number of atoms: 4012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4012 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 15, 'TRANS': 478} Chain breaks: 1 Chain: "C" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4912 Classifications: {'peptide': 626} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 586} Chain: "D" Number of atoms: 9433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9433 Classifications: {'peptide': 1194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1133} Chain breaks: 2 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 813 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 13} Link IDs: {'rna2p': 5, 'rna3p': 32} Chain: "B" Number of atoms: 88 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 3, 'ANP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Conformer: "B" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 3, 'ANP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} bond proxies already assigned to first conformer: 33 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12234 SG CYS D 338 55.815 85.059 83.714 1.00 79.24 S ATOM 12277 SG CYS D 344 57.261 86.078 87.075 1.00 91.86 S ATOM 12327 SG CYS D 351 55.477 88.766 85.027 1.00 68.72 S ATOM 12346 SG CYS D 354 53.478 86.376 86.296 1.00 73.62 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASAM B 605 " occ=0.50 ... (52 atoms not shown) pdb=" O4'BSAM B 605 " occ=0.50 Time building chain proxies: 3.33, per 1000 atoms: 0.17 Number of scatterers: 20118 At special positions: 0 Unit cell: (113.544, 119.52, 175.296, 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 63 16.00 P 80 15.00 Mg 4 11.99 O 4074 8.00 N 3538 7.00 C 12358 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: 1.48 Conformation dependent library (CDL) restraints added in 780.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 338 " 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 354 " Number of angles added : 6 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 40 sheets defined 35.7% alpha, 23.3% beta 28 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'B' and resid 21 through 39 removed outlier: 4.412A pdb=" N MET B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.654A pdb=" N TYR B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 187 removed outlier: 3.506A pdb=" N LEU B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 240 through 254 removed outlier: 5.055A pdb=" N THR B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) 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 326 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 355 through 373 removed outlier: 4.733A pdb=" N TRP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.597A pdb=" N LYS B 425 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS B 426 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 486 through 499 removed outlier: 4.032A pdb=" N ILE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.742A 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 560 removed outlier: 5.647A pdb=" N ASP B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B 560 " --> pdb=" O TRP B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 66 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.588A pdb=" N SER C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 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 335 through 339 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: 3.956A 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 Processing helix chain 'C' and resid 573 through 580 Processing helix chain 'C' and resid 587 through 591 removed outlier: 3.578A pdb=" N GLU C 590 " --> pdb=" O VAL C 587 " (cutoff:3.500A) 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 86 through 93 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.934A 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: 3.568A 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: 3.536A 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: 3.762A 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 669 through 673 removed outlier: 3.531A pdb=" N ALA D 673 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 691 removed outlier: 3.576A 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 773 removed outlier: 3.773A pdb=" N GLN D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 796 Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 806 through 811 removed outlier: 3.526A pdb=" N CYS D 809 " --> pdb=" O ASP D 806 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS D 810 " --> pdb=" O ASN D 807 " (cutoff:3.500A) 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 905 removed outlier: 3.764A pdb=" N ARG D 904 " --> pdb=" O LYS D 901 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP D 905 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 928 removed outlier: 3.707A pdb=" N ILE D 927 " --> pdb=" O PRO D 923 " (cutoff:3.500A) removed outlier: 3.707A 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 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 1151 removed outlier: 3.919A pdb=" N THR D1150 " --> pdb=" O SER D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1152 through 1164 removed outlier: 3.605A 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: 4.196A pdb=" N PHE D1190 " --> pdb=" O ASN D1186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 117 through 119 removed outlier: 5.649A pdb=" N THR B 117 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 128 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.555A 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 213 through 216 removed outlier: 4.241A pdb=" N ASN B 224 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 345 removed outlier: 6.313A pdb=" N ILE B 350 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP B 344 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU B 348 " --> pdb=" O TRP B 344 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS B 391 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ALA B 431 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 393 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLN B 433 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 395 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 333 Processing sheet with id=AA6, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.305A pdb=" N LYS C 13 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.092A 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: 3.598A pdb=" N THR C 121 " --> pdb=" O HIS C 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS C 133 " --> pdb=" O THR C 121 " (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: 5.275A pdb=" N THR C 437 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 237 through 239 removed outlier: 6.754A pdb=" N PHE C 238 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 392 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LYS C 383 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ASP C 375 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN C 385 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 4.652A 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: 6.923A pdb=" N VAL C 547 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR C 511 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 6.555A 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: 3.501A pdb=" N VAL D 115 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.419A 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: 3.501A pdb=" N VAL D 115 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG D 166 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THR D 22 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN D 215 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 24 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 6.388A 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: 5.357A pdb=" N GLU D 35 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 143 removed outlier: 10.573A pdb=" N TYR D 136 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N TYR D 157 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N GLU D 138 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N LEU D 155 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N SER D 140 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ALA D 153 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR D 142 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 312 through 313 Processing sheet with id=AC6, first strand: chain 'D' and resid 312 through 313 Processing sheet with id=AC7, first strand: chain 'D' and resid 281 through 282 removed outlier: 6.467A pdb=" N HIS D 301 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N PHE D 406 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 281 through 282 removed outlier: 5.945A pdb=" N ALA D 399 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 518 through 519 Processing sheet with id=AD1, first strand: chain 'D' and resid 523 through 526 Processing sheet with id=AD2, first strand: chain 'D' and resid 537 through 538 Processing sheet with id=AD3, first strand: chain 'D' and resid 914 through 916 removed outlier: 6.652A pdb=" N SER D1036 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA D 575 " --> pdb=" O SER D1036 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR D1038 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 573 " --> pdb=" O TYR D1038 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS D1040 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 571 " --> pdb=" O HIS D1040 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D1042 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 569 " --> pdb=" O ASP D1042 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN D1044 " --> pdb=" O GLY D 567 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY D 567 " --> pdb=" O ASN D1044 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 914 through 916 removed outlier: 6.652A pdb=" N SER D1036 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA D 575 " --> pdb=" O SER D1036 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR D1038 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 573 " --> pdb=" O TYR D1038 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS D1040 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 571 " --> pdb=" O HIS D1040 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D1042 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 569 " --> pdb=" O ASP D1042 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN D1044 " --> pdb=" O GLY D 567 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY D 567 " --> pdb=" O ASN D1044 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS D 572 " --> pdb=" O ILE D1083 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE D1083 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR D 574 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE D1081 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 582 through 585 removed outlier: 4.307A pdb=" N GLY D 584 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS D 596 " --> pdb=" O ARG D1027 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 602 through 603 Processing sheet with id=AD7, first strand: chain 'D' and resid 639 through 641 Processing sheet with id=AD8, first strand: chain 'D' and resid 776 through 777 removed outlier: 6.951A pdb=" N ILE D 651 " --> pdb=" O MET D 666 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 650 " --> pdb=" O PHE D 843 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 674 through 676 Processing sheet with id=AE1, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 Processing sheet with id=AE3, first strand: chain 'D' and resid 893 through 895 Processing sheet with id=AE4, first strand: chain 'D' and resid 955 through 957 769 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 1.95 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: 4238 1.33 - 1.45: 6175 1.45 - 1.58: 10039 1.58 - 1.70: 158 1.70 - 1.82: 98 Bond restraints: 20708 Sorted by residual: bond pdb=" C8 G A 39 " pdb=" N7 G A 39 " ideal model delta sigma weight residual 1.305 1.384 -0.079 6.00e-03 2.78e+04 1.73e+02 bond pdb=" N1 G A 39 " pdb=" C2 G A 39 " ideal model delta sigma weight residual 1.373 1.451 -0.078 8.00e-03 1.56e+04 9.40e+01 bond pdb=" C5 G A 39 " pdb=" C4 G A 39 " ideal model delta sigma weight residual 1.379 1.444 -0.065 7.00e-03 2.04e+04 8.60e+01 bond pdb=" N3B ANP B 604 " pdb=" PG ANP B 604 " ideal model delta sigma weight residual 1.795 1.617 0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C5 G A 39 " pdb=" C6 G A 39 " ideal model delta sigma weight residual 1.419 1.484 -0.065 1.00e-02 1.00e+04 4.17e+01 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 27269 3.54 - 7.09: 1044 7.09 - 10.63: 79 10.63 - 14.17: 9 14.17 - 17.72: 2 Bond angle restraints: 28403 Sorted by residual: angle pdb=" C5 G A 39 " pdb=" C6 G A 39 " pdb=" N1 G A 39 " ideal model delta sigma weight residual 111.50 107.27 4.23 5.00e-01 4.00e+00 7.16e+01 angle pdb=" O3' U A 3 " pdb=" P G A 4 " pdb=" O5' G A 4 " ideal model delta sigma weight residual 104.00 88.39 15.61 1.90e+00 2.77e-01 6.75e+01 angle pdb=" CG MET D 210 " pdb=" SD MET D 210 " pdb=" CE MET D 210 " ideal model delta sigma weight residual 100.90 83.18 17.72 2.20e+00 2.07e-01 6.48e+01 angle pdb=" C4' A A 27 " pdb=" O4' A A 27 " pdb=" C1' A A 27 " ideal model delta sigma weight residual 109.70 104.39 5.31 7.00e-01 2.04e+00 5.75e+01 angle pdb=" CA ASP B 307 " pdb=" CB ASP B 307 " pdb=" CG ASP B 307 " ideal model delta sigma weight residual 112.60 120.15 -7.55 1.00e+00 1.00e+00 5.70e+01 ... (remaining 28398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 11977 31.11 - 62.21: 485 62.21 - 93.32: 120 93.32 - 124.42: 0 124.42 - 155.53: 1 Dihedral angle restraints: 12583 sinusoidal: 5917 harmonic: 6666 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 76.47 155.53 1 1.70e+01 3.46e-03 6.35e+01 dihedral pdb=" CA VAL B 244 " pdb=" C VAL B 244 " pdb=" N TYR B 245 " pdb=" CA TYR B 245 " ideal model delta harmonic sigma weight residual -180.00 -147.94 -32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA GLU D1097 " pdb=" C GLU D1097 " pdb=" N ALA D1098 " pdb=" CA ALA D1098 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 12580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2648 0.115 - 0.230: 433 0.230 - 0.345: 34 0.345 - 0.460: 4 0.460 - 0.575: 3 Chirality restraints: 3122 Sorted by residual: chirality pdb=" P U E 1 " pdb=" OP1 U E 1 " pdb=" OP2 U E 1 " pdb=" O5' U E 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.57 2.00e-01 2.50e+01 8.26e+00 chirality pdb=" P C E 24 " pdb=" OP1 C E 24 " pdb=" OP2 C E 24 " pdb=" O5' C E 24 " both_signs ideal model delta sigma weight residual True 2.41 -1.84 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA ASN D 158 " pdb=" N ASN D 158 " pdb=" C ASN D 158 " pdb=" CB ASN D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 3119 not shown) Planarity restraints: 3415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 39 " -0.079 2.00e-02 2.50e+03 5.19e-02 8.07e+01 pdb=" N9 G A 39 " -0.021 2.00e-02 2.50e+03 pdb=" C8 G A 39 " 0.047 2.00e-02 2.50e+03 pdb=" N7 G A 39 " 0.048 2.00e-02 2.50e+03 pdb=" C5 G A 39 " 0.055 2.00e-02 2.50e+03 pdb=" C6 G A 39 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 39 " -0.120 2.00e-02 2.50e+03 pdb=" N1 G A 39 " 0.044 2.00e-02 2.50e+03 pdb=" C2 G A 39 " 0.029 2.00e-02 2.50e+03 pdb=" N2 G A 39 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G A 39 " -0.020 2.00e-02 2.50e+03 pdb=" C4 G A 39 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 32 " 0.106 2.00e-02 2.50e+03 4.61e-02 5.85e+01 pdb=" N9 A E 32 " -0.091 2.00e-02 2.50e+03 pdb=" C8 A E 32 " -0.016 2.00e-02 2.50e+03 pdb=" N7 A E 32 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A E 32 " -0.012 2.00e-02 2.50e+03 pdb=" C6 A E 32 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A E 32 " 0.052 2.00e-02 2.50e+03 pdb=" N1 A E 32 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A E 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A E 32 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A E 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 13 " -0.104 2.00e-02 2.50e+03 5.08e-02 5.81e+01 pdb=" N1 C A 13 " 0.022 2.00e-02 2.50e+03 pdb=" C2 C A 13 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C A 13 " 0.046 2.00e-02 2.50e+03 pdb=" N3 C A 13 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C A 13 " -0.017 2.00e-02 2.50e+03 pdb=" N4 C A 13 " -0.056 2.00e-02 2.50e+03 pdb=" C5 C A 13 " 0.024 2.00e-02 2.50e+03 pdb=" C6 C A 13 " 0.076 2.00e-02 2.50e+03 ... (remaining 3412 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 101 2.53 - 3.12: 14734 3.12 - 3.72: 31890 3.72 - 4.31: 47750 4.31 - 4.90: 78083 Nonbonded interactions: 172558 Sorted by model distance: nonbonded pdb=" OD1 ASP B 347 " pdb="MG MG B 602 " model vdw 1.938 2.170 nonbonded pdb=" OD2 ASP B 347 " pdb="MG MG B 601 " model vdw 2.002 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ANP B 604 " model vdw 2.007 2.170 nonbonded pdb=" O SER D 495 " pdb=" OG1 THR D 535 " model vdw 2.069 3.040 nonbonded pdb="MG MG B 601 " pdb=" O2B ANP B 604 " model vdw 2.078 2.170 ... (remaining 172553 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=0.50 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 0.178 20712 Z= 0.647 Angle : 1.586 17.716 28409 Z= 1.009 Chirality : 0.085 0.575 3122 Planarity : 0.010 0.117 3415 Dihedral : 17.003 155.531 8307 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 6.00 % Favored : 91.56 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2302 helix: 0.62 (0.19), residues: 640 sheet: 0.01 (0.24), residues: 413 loop : -0.13 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.006 ARG D 316 TYR 0.056 0.008 TYR C 600 PHE 0.072 0.009 PHE D1147 TRP 0.075 0.010 TRP B 331 HIS 0.026 0.005 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.65 (20708) covalent geometry : angle 1.58213 / 1.01 (28403) hydrogen bonds : bond 0.18558 / 19.49 ( 806) hydrogen bonds : angle 6.64865 / 7.19 ( 2169) metal coordination : bond 0.02580 / 2.04 ( 4) metal coordination : angle 7.88021 / 15.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 LEU cc_start: 0.6121 (tp) cc_final: 0.5625 (tm) REVERT: B 34 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5474 (mm-30) REVERT: B 37 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5857 (mm-30) REVERT: B 38 ASP cc_start: 0.4865 (m-30) cc_final: 0.4375 (m-30) REVERT: B 42 LYS cc_start: 0.5410 (ttpp) cc_final: 0.5177 (mmtm) REVERT: B 149 ASP cc_start: 0.5980 (m-30) cc_final: 0.5439 (m-30) REVERT: B 161 ASP cc_start: 0.6787 (m-30) cc_final: 0.6339 (m-30) REVERT: B 199 LYS cc_start: 0.8204 (tptt) cc_final: 0.7499 (tppt) REVERT: B 205 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7829 (p0) REVERT: B 213 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 228 ILE cc_start: 0.8029 (mt) cc_final: 0.7732 (mm) REVERT: B 259 LYS cc_start: 0.6677 (mtpt) cc_final: 0.6131 (tptt) REVERT: B 262 LYS cc_start: 0.7064 (mtpt) cc_final: 0.6328 (ptpt) REVERT: B 325 ILE cc_start: 0.6269 (mt) cc_final: 0.6046 (mm) REVERT: B 326 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5634 (pttp) REVERT: B 327 GLU cc_start: 0.4755 (OUTLIER) cc_final: 0.4524 (pp20) REVERT: B 370 ARG cc_start: 0.6940 (tpt-90) cc_final: 0.5791 (ttp-170) REVERT: B 412 ARG cc_start: 0.6704 (mtp-110) cc_final: 0.5749 (mtt180) REVERT: B 427 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: B 429 MET cc_start: 0.8557 (mmp) cc_final: 0.8276 (mmm) REVERT: B 450 LYS cc_start: 0.6927 (mttm) cc_final: 0.6536 (mtpt) REVERT: B 454 LYS cc_start: 0.7381 (tttt) cc_final: 0.7077 (tttp) REVERT: B 458 ASP cc_start: 0.7414 (p0) cc_final: 0.7201 (m-30) REVERT: B 471 GLU cc_start: 0.6636 (tp30) cc_final: 0.5609 (pm20) REVERT: B 484 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 495 GLN cc_start: 0.7714 (tt0) cc_final: 0.7331 (tm-30) REVERT: B 504 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6413 (mm-30) REVERT: B 510 LYS cc_start: 0.6962 (mttt) cc_final: 0.6748 (mttp) REVERT: B 523 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5929 (tp30) REVERT: C 7 LYS cc_start: 0.7523 (mttt) cc_final: 0.6908 (mmpt) REVERT: C 13 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7654 (ttmm) REVERT: C 70 MET cc_start: 0.5343 (mmm) cc_final: 0.4983 (mmp) REVERT: C 275 LYS cc_start: 0.6666 (tppp) cc_final: 0.5892 (mmtt) REVERT: C 284 LEU cc_start: 0.7585 (mp) cc_final: 0.7384 (mt) REVERT: C 323 GLU cc_start: 0.7432 (tp30) cc_final: 0.7130 (tp30) REVERT: C 358 GLU cc_start: 0.6840 (mp0) cc_final: 0.6252 (mp0) REVERT: C 382 LYS cc_start: 0.7548 (tttm) cc_final: 0.7311 (tttt) REVERT: C 390 GLU cc_start: 0.7817 (tt0) cc_final: 0.7163 (mt-10) REVERT: C 454 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: C 457 SER cc_start: 0.8101 (m) cc_final: 0.7872 (t) REVERT: C 489 GLU cc_start: 0.6599 (mp0) cc_final: 0.6309 (mt-10) REVERT: C 496 LYS cc_start: 0.7341 (tttt) cc_final: 0.6981 (tttm) REVERT: C 516 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8044 (pttt) REVERT: C 528 GLN cc_start: 0.7771 (mt0) cc_final: 0.7377 (mt0) REVERT: C 529 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6275 (tptt) REVERT: C 541 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7941 (mt-10) REVERT: C 549 GLU cc_start: 0.6705 (tt0) cc_final: 0.6320 (tt0) REVERT: C 554 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.6108 (p0) REVERT: C 566 LEU cc_start: 0.7427 (tp) cc_final: 0.7201 (mt) REVERT: C 567 GLN cc_start: 0.6664 (mm-40) cc_final: 0.6087 (tt0) REVERT: C 575 GLU cc_start: 0.6630 (tt0) cc_final: 0.6147 (tp30) REVERT: C 583 GLU cc_start: 0.6611 (pt0) cc_final: 0.6179 (pt0) REVERT: C 608 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6949 (mp0) REVERT: D 16 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7101 (mtt180) REVERT: D 18 LYS cc_start: 0.7271 (ttmm) cc_final: 0.6894 (ttpt) REVERT: D 90 GLU cc_start: 0.6016 (mt-10) cc_final: 0.5531 (mm-30) REVERT: D 102 GLU cc_start: 0.6674 (mt-10) cc_final: 0.5743 (tp30) REVERT: D 131 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: D 194 THR cc_start: 0.6994 (m) cc_final: 0.6542 (p) REVERT: D 202 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6841 (mt-10) REVERT: D 210 MET cc_start: 0.8256 (mmt) cc_final: 0.7840 (mmt) REVERT: D 356 MET cc_start: 0.8310 (ttt) cc_final: 0.7985 (ttp) REVERT: D 373 TYR cc_start: 0.7893 (t80) cc_final: 0.7569 (t80) REVERT: D 412 LYS cc_start: 0.7642 (mtpm) cc_final: 0.6948 (mmmt) REVERT: D 418 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7233 (ttmt) REVERT: D 461 GLU cc_start: 0.6911 (tt0) cc_final: 0.6699 (tt0) REVERT: D 488 ASP cc_start: 0.5842 (p0) cc_final: 0.5627 (m-30) REVERT: D 490 TRP cc_start: 0.6425 (p-90) cc_final: 0.6081 (p90) REVERT: D 541 LYS cc_start: 0.7005 (mmtp) cc_final: 0.6213 (mtmt) REVERT: D 587 GLU cc_start: 0.7570 (pt0) cc_final: 0.7278 (mm-30) REVERT: D 592 ASP cc_start: 0.6442 (m-30) cc_final: 0.5977 (p0) REVERT: D 596 LYS cc_start: 0.7543 (mmtm) cc_final: 0.6855 (mttt) REVERT: D 646 ARG cc_start: 0.6785 (mtp-110) cc_final: 0.6580 (mtt90) REVERT: D 662 ARG cc_start: 0.6326 (mtt-85) cc_final: 0.5738 (mtp-110) REVERT: D 672 ASN cc_start: 0.5243 (OUTLIER) cc_final: 0.5035 (p0) REVERT: D 686 MET cc_start: 0.4816 (mtp) cc_final: 0.4549 (mtt) REVERT: D 815 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6641 (mt) REVERT: D 836 ARG cc_start: 0.5916 (mtt90) cc_final: 0.5545 (mtp85) REVERT: D 873 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6168 (mp0) REVERT: D 881 LYS cc_start: 0.7630 (mmtp) cc_final: 0.7283 (mmtt) REVERT: D 884 TRP cc_start: 0.7908 (m100) cc_final: 0.7584 (m100) REVERT: D 931 ASP cc_start: 0.6889 (m-30) cc_final: 0.6287 (t0) REVERT: D 959 SER cc_start: 0.6640 (p) cc_final: 0.6424 (m) REVERT: D 1010 HIS cc_start: 0.6794 (m90) cc_final: 0.6480 (m90) REVERT: D 1097 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5323 (pt0) REVERT: D 1139 ARG cc_start: 0.6009 (mtt90) cc_final: 0.5807 (mpt180) REVERT: D 1141 ASP cc_start: 0.7103 (m-30) cc_final: 0.6374 (p0) REVERT: D 1160 GLU cc_start: 0.8123 (tp30) cc_final: 0.6996 (mp0) REVERT: D 1199 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6238 (m-30) REVERT: D 1222 THR cc_start: 0.7389 (m) cc_final: 0.7184 (p) REVERT: D 1227 ASN cc_start: 0.6993 (m110) cc_final: 0.6484 (t0) REVERT: D 1230 GLU cc_start: 0.7399 (pt0) cc_final: 0.7162 (tp30) outliers start: 48 outliers final: 8 residues processed: 395 average time/residue: 0.6155 time to fit residues: 271.5248 Evaluate side-chains 291 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 672 ASN Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1199 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 428 ASN B 482 GLN B 496 GLN C 92 ASN C 139 ASN C 263 GLN C 288 HIS C 329 ASN C 427 GLN C 531 HIS D 158 ASN D 188 GLN D 195 ASN D 392 HIS D 423 ASN D 486 HIS D 520 HIS D 604 ASN D 672 ASN D 744 ASN D1109 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.165569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137295 restraints weight = 19628.460| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.55 r_work: 0.3137 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20712 Z= 0.143 Angle : 0.621 7.815 28409 Z= 0.339 Chirality : 0.045 0.217 3122 Planarity : 0.004 0.041 3415 Dihedral : 15.467 161.386 3847 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.85 % Allowed : 9.66 % Favored : 87.49 % 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: 0.82 (0.17), residues: 2302 helix: 1.51 (0.20), residues: 636 sheet: 0.25 (0.24), residues: 393 loop : 0.25 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.020 0.002 TYR D 786 PHE 0.019 0.002 PHE B 127 TRP 0.017 0.001 TRP B 360 HIS 0.007 0.001 HIS B 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (20708) covalent geometry : angle 0.61944 / 0.34 (28403) hydrogen bonds : bond 0.05871 / 6.15 ( 806) hydrogen bonds : angle 5.12530 / 5.69 ( 2169) metal coordination : bond 0.00401 / 0.36 ( 4) metal coordination : angle 3.00142 / 5.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 5 LEU cc_start: 0.7326 (tp) cc_final: 0.7096 (tm) REVERT: B 8 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: B 149 ASP cc_start: 0.7191 (m-30) cc_final: 0.6826 (m-30) REVERT: B 259 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7423 (tptt) REVERT: B 262 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6988 (ptpt) REVERT: B 263 ASP cc_start: 0.8055 (p0) cc_final: 0.7842 (p0) REVERT: B 370 ARG cc_start: 0.7674 (tpt-90) cc_final: 0.6813 (ttp-170) REVERT: B 412 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7684 (mtt-85) REVERT: B 421 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7342 (pt) REVERT: B 423 ASN cc_start: 0.8206 (m110) cc_final: 0.7896 (t0) REVERT: B 425 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: B 427 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7817 (mtp180) REVERT: B 450 LYS cc_start: 0.8663 (mttm) cc_final: 0.8407 (mtpt) REVERT: B 454 LYS cc_start: 0.8682 (tttt) cc_final: 0.8438 (tttp) REVERT: B 484 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 504 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8057 (mm-30) REVERT: B 523 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6778 (tp30) REVERT: B 526 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: C 70 MET cc_start: 0.6253 (mmm) cc_final: 0.6032 (mmp) REVERT: C 275 LYS cc_start: 0.7788 (tppp) cc_final: 0.7182 (mmtt) REVERT: C 323 GLU cc_start: 0.7873 (tp30) cc_final: 0.7627 (tp30) REVERT: C 397 LYS cc_start: 0.7785 (mttp) cc_final: 0.7411 (mttm) REVERT: C 412 TYR cc_start: 0.5517 (t80) cc_final: 0.5096 (t80) REVERT: C 454 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: C 541 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8409 (mt-10) REVERT: C 560 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7245 (ptt90) REVERT: C 575 GLU cc_start: 0.7469 (tt0) cc_final: 0.7248 (tp30) REVERT: D 16 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7313 (mtt180) REVERT: D 47 ASP cc_start: 0.6201 (m-30) cc_final: 0.5594 (t70) REVERT: D 76 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.6737 (ttp-170) REVERT: D 102 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7310 (tp30) REVERT: D 194 THR cc_start: 0.8283 (m) cc_final: 0.7965 (p) REVERT: D 407 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: D 412 LYS cc_start: 0.8839 (mtpm) cc_final: 0.8569 (mmmt) REVERT: D 541 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7841 (mmpt) REVERT: D 596 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8380 (mttt) REVERT: D 666 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7154 (mmm) REVERT: D 669 ASN cc_start: 0.7540 (t0) cc_final: 0.7237 (t0) REVERT: D 672 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5163 (p0) REVERT: D 686 MET cc_start: 0.5966 (mtp) cc_final: 0.5638 (mtt) REVERT: D 836 ARG cc_start: 0.7163 (mtt90) cc_final: 0.6768 (mtp180) REVERT: D 852 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: D 853 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7786 (pt) REVERT: D 874 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: D 884 TRP cc_start: 0.8652 (m100) cc_final: 0.8419 (m100) REVERT: D 931 ASP cc_start: 0.8042 (m-30) cc_final: 0.7793 (t0) REVERT: D 1097 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6018 (pt0) REVERT: D 1199 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6635 (m-30) outliers start: 56 outliers final: 13 residues processed: 322 average time/residue: 0.6460 time to fit residues: 231.5076 Evaluate side-chains 263 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 672 ASN Chi-restraints excluded: chain D residue 725 CYS Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 1199 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 27 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 0.0370 chunk 207 optimal weight: 5.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 GLN C 36 GLN C 263 GLN C 427 GLN C 528 GLN C 567 GLN D 195 ASN D 392 HIS D 665 GLN D 763 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133480 restraints weight = 19455.337| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.60 r_work: 0.3064 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20712 Z= 0.190 Angle : 0.633 7.966 28409 Z= 0.340 Chirality : 0.047 0.222 3122 Planarity : 0.005 0.043 3415 Dihedral : 14.934 162.162 3815 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.41 % Allowed : 11.39 % Favored : 85.21 % 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: 0.71 (0.17), residues: 2302 helix: 1.35 (0.20), residues: 637 sheet: 0.18 (0.24), residues: 396 loop : 0.23 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 269 TYR 0.019 0.002 TYR D 786 PHE 0.021 0.002 PHE D1147 TRP 0.018 0.002 TRP B 360 HIS 0.008 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (20708) covalent geometry : angle 0.63150 / 0.34 (28403) hydrogen bonds : bond 0.05802 / 6.05 ( 806) hydrogen bonds : angle 5.03596 / 5.64 ( 2169) metal coordination : bond 0.00310 / 0.28 ( 4) metal coordination : angle 3.11575 / 5.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.781 Fit side-chains REVERT: B 8 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: B 149 ASP cc_start: 0.7338 (m-30) cc_final: 0.7078 (m-30) REVERT: B 259 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7438 (tptt) REVERT: B 262 LYS cc_start: 0.7312 (mtpt) cc_final: 0.6938 (ptpt) REVERT: B 265 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 326 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5849 (pttp) REVERT: B 332 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7594 (mmm-85) REVERT: B 370 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.6979 (ttm170) REVERT: B 412 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7847 (mtt-85) REVERT: B 423 ASN cc_start: 0.8307 (m110) cc_final: 0.7930 (t0) REVERT: B 425 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8359 (mmtm) REVERT: B 427 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7898 (mtp180) REVERT: B 439 ASP cc_start: 0.8178 (p0) cc_final: 0.7905 (m-30) REVERT: B 450 LYS cc_start: 0.8674 (mttm) cc_final: 0.8417 (mtpt) REVERT: B 454 LYS cc_start: 0.8791 (tttt) cc_final: 0.8556 (tttp) REVERT: B 484 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 504 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8090 (mm-30) REVERT: B 523 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6572 (tp30) REVERT: B 526 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: C 275 LYS cc_start: 0.7918 (tppp) cc_final: 0.7349 (mmtt) REVERT: C 323 GLU cc_start: 0.8063 (tp30) cc_final: 0.7781 (tp30) REVERT: C 412 TYR cc_start: 0.6186 (t80) cc_final: 0.5813 (t80) REVERT: C 454 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: C 560 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7392 (ptt90) REVERT: D 47 ASP cc_start: 0.6220 (m-30) cc_final: 0.5635 (t70) REVERT: D 76 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7238 (ttp-170) REVERT: D 102 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7292 (tp30) REVERT: D 194 THR cc_start: 0.8449 (m) cc_final: 0.8192 (p) REVERT: D 221 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7516 (tp) REVERT: D 407 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: D 412 LYS cc_start: 0.8922 (mtpm) cc_final: 0.8610 (mmmt) REVERT: D 541 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7817 (mmtt) REVERT: D 596 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8422 (mtmt) REVERT: D 666 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7329 (mmm) REVERT: D 669 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7261 (t0) REVERT: D 672 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5469 (p0) REVERT: D 686 MET cc_start: 0.6114 (mtp) cc_final: 0.5890 (mtt) REVERT: D 836 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6857 (mtp180) REVERT: D 852 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: D 853 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8040 (pt) REVERT: D 874 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: D 884 TRP cc_start: 0.8702 (m100) cc_final: 0.8483 (m100) REVERT: D 931 ASP cc_start: 0.8109 (m-30) cc_final: 0.7771 (t0) REVERT: D 1097 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6054 (pt0) REVERT: D 1199 ASP cc_start: 0.7465 (m-30) cc_final: 0.6910 (m-30) outliers start: 67 outliers final: 21 residues processed: 286 average time/residue: 0.7259 time to fit residues: 230.3414 Evaluate side-chains 269 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 672 ASN Chi-restraints excluded: chain D residue 725 CYS Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 169 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN B 482 GLN C 36 GLN C 263 GLN C 391 GLN C 427 GLN D 50 GLN D 195 ASN D 392 HIS D 422 GLN D1105 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.163309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135048 restraints weight = 19534.721| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.57 r_work: 0.3082 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20712 Z= 0.144 Angle : 0.558 7.946 28409 Z= 0.301 Chirality : 0.044 0.213 3122 Planarity : 0.004 0.050 3415 Dihedral : 14.735 165.843 3809 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.41 % Allowed : 12.20 % Favored : 84.39 % 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: 0.78 (0.17), residues: 2302 helix: 1.45 (0.20), residues: 639 sheet: 0.20 (0.25), residues: 393 loop : 0.25 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 414 TYR 0.017 0.002 TYR D 786 PHE 0.016 0.002 PHE D1147 TRP 0.019 0.001 TRP D 429 HIS 0.008 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (20708) covalent geometry : angle 0.55633 / 0.30 (28403) hydrogen bonds : bond 0.04979 / 5.21 ( 806) hydrogen bonds : angle 4.87903 / 5.48 ( 2169) metal coordination : bond 0.00266 / 0.24 ( 4) metal coordination : angle 3.02375 / 5.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 259 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7306 (tptt) REVERT: B 262 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6943 (ptpt) REVERT: B 265 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: B 312 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6259 (pp20) REVERT: B 326 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5717 (pttp) REVERT: B 332 ARG cc_start: 0.7791 (mmt90) cc_final: 0.7490 (mmm-85) REVERT: B 370 ARG cc_start: 0.7805 (tpt-90) cc_final: 0.6908 (ttm170) REVERT: B 371 GLU cc_start: 0.7803 (pt0) cc_final: 0.7594 (pt0) REVERT: B 412 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7791 (mtt-85) REVERT: B 423 ASN cc_start: 0.8233 (m110) cc_final: 0.7944 (t0) REVERT: B 439 ASP cc_start: 0.8123 (p0) cc_final: 0.7901 (m-30) REVERT: B 450 LYS cc_start: 0.8712 (mttm) cc_final: 0.8436 (mtpt) REVERT: B 454 LYS cc_start: 0.8812 (tttt) cc_final: 0.8582 (tttp) REVERT: B 484 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8114 (mt-10) REVERT: B 504 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8047 (mm-30) REVERT: B 523 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6422 (tp30) REVERT: B 526 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: C 181 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: C 323 GLU cc_start: 0.8013 (tp30) cc_final: 0.7714 (tp30) REVERT: C 367 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: C 412 TYR cc_start: 0.6357 (t80) cc_final: 0.5972 (t80) REVERT: C 454 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: C 549 GLU cc_start: 0.7778 (tt0) cc_final: 0.7545 (tt0) REVERT: C 560 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7410 (ptt90) REVERT: D 47 ASP cc_start: 0.6257 (m-30) cc_final: 0.5668 (t70) REVERT: D 102 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7292 (tp30) REVERT: D 194 THR cc_start: 0.8449 (m) cc_final: 0.8124 (p) REVERT: D 221 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7629 (tp) REVERT: D 407 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: D 412 LYS cc_start: 0.8897 (mtpm) cc_final: 0.8605 (mmmt) REVERT: D 541 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7762 (mmtt) REVERT: D 596 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8390 (mtmt) REVERT: D 666 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7355 (mmm) REVERT: D 669 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7274 (t0) REVERT: D 672 ASN cc_start: 0.5859 (OUTLIER) cc_final: 0.5386 (p0) REVERT: D 836 ARG cc_start: 0.7247 (mtt90) cc_final: 0.6787 (mtp180) REVERT: D 852 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: D 853 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8077 (pt) REVERT: D 931 ASP cc_start: 0.8099 (m-30) cc_final: 0.7742 (t0) REVERT: D 1097 GLU cc_start: 0.6572 (mt-10) cc_final: 0.5846 (pt0) REVERT: D 1199 ASP cc_start: 0.7511 (m-30) cc_final: 0.6899 (m-30) outliers start: 67 outliers final: 25 residues processed: 277 average time/residue: 0.6591 time to fit residues: 203.6653 Evaluate side-chains 267 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 672 ASN Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 928 ARG Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 66 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 GLN D 50 GLN D 195 ASN D 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.161786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133812 restraints weight = 19607.239| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.54 r_work: 0.3109 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20712 Z= 0.152 Angle : 0.574 8.751 28409 Z= 0.306 Chirality : 0.044 0.218 3122 Planarity : 0.005 0.052 3415 Dihedral : 14.613 166.162 3801 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.15 % Allowed : 13.22 % Favored : 83.63 % 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: 0.74 (0.17), residues: 2302 helix: 1.45 (0.20), residues: 641 sheet: 0.22 (0.24), residues: 397 loop : 0.19 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1214 TYR 0.017 0.002 TYR D 786 PHE 0.016 0.002 PHE D1147 TRP 0.019 0.001 TRP D 429 HIS 0.007 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (20708) covalent geometry : angle 0.57191 / 0.31 (28403) hydrogen bonds : bond 0.05032 / 5.26 ( 806) hydrogen bonds : angle 4.87100 / 5.48 ( 2169) metal coordination : bond 0.00254 / 0.23 ( 4) metal coordination : angle 3.09312 / 5.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.785 Fit side-chains REVERT: B 259 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7275 (tptt) REVERT: B 262 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6881 (ptpt) REVERT: B 265 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: B 326 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5650 (pttp) REVERT: B 370 ARG cc_start: 0.7807 (tpt-90) cc_final: 0.6801 (ttp-170) REVERT: B 371 GLU cc_start: 0.7920 (pt0) cc_final: 0.7686 (pt0) REVERT: B 412 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7753 (mtt-85) REVERT: B 423 ASN cc_start: 0.8214 (m110) cc_final: 0.7917 (t0) REVERT: B 425 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8364 (mmtm) REVERT: B 439 ASP cc_start: 0.8241 (p0) cc_final: 0.7937 (m-30) REVERT: B 450 LYS cc_start: 0.8694 (mttm) cc_final: 0.8264 (tptp) REVERT: B 454 LYS cc_start: 0.8862 (tttt) cc_final: 0.8633 (tttp) REVERT: B 484 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 504 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8036 (mm-30) REVERT: B 523 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6374 (tp30) REVERT: B 526 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: C 136 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8757 (mtt) REVERT: C 181 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8538 (ttmm) REVERT: C 323 GLU cc_start: 0.8078 (tp30) cc_final: 0.7754 (tp30) REVERT: C 367 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: C 414 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6729 (mtm110) REVERT: C 427 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6853 (mp-120) REVERT: C 559 GLN cc_start: 0.7691 (tt0) cc_final: 0.7298 (tt0) REVERT: C 560 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7424 (ttp80) REVERT: C 572 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7772 (tp) REVERT: C 584 SER cc_start: 0.8029 (p) cc_final: 0.7746 (t) REVERT: D 47 ASP cc_start: 0.6067 (m-30) cc_final: 0.5522 (t70) REVERT: D 102 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7042 (tp30) REVERT: D 194 THR cc_start: 0.8441 (m) cc_final: 0.8096 (p) REVERT: D 232 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: D 407 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: D 412 LYS cc_start: 0.8898 (mtpm) cc_final: 0.8594 (mmmt) REVERT: D 422 GLN cc_start: 0.6680 (mm110) cc_final: 0.6132 (tt0) REVERT: D 541 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7722 (mmtt) REVERT: D 596 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8376 (mtmt) REVERT: D 666 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7327 (mmm) REVERT: D 669 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7353 (t0) REVERT: D 672 ASN cc_start: 0.5871 (OUTLIER) cc_final: 0.5493 (p0) REVERT: D 795 LEU cc_start: 0.8760 (mp) cc_final: 0.8395 (mp) REVERT: D 836 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6683 (mtp180) REVERT: D 844 ASP cc_start: 0.8121 (t0) cc_final: 0.7872 (t70) REVERT: D 852 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: D 853 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8207 (pt) REVERT: D 931 ASP cc_start: 0.8096 (m-30) cc_final: 0.7686 (t0) REVERT: D 1097 GLU cc_start: 0.6647 (mt-10) cc_final: 0.5818 (pt0) REVERT: D 1199 ASP cc_start: 0.7546 (m-30) cc_final: 0.6889 (m-30) outliers start: 62 outliers final: 27 residues processed: 276 average time/residue: 0.7426 time to fit residues: 229.0372 Evaluate side-chains 274 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 672 ASN Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 928 ARG Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 230 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 224 optimal weight: 0.0270 chunk 130 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN D 50 GLN D 195 ASN D 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133826 restraints weight = 19357.074| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.53 r_work: 0.3076 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20712 Z= 0.152 Angle : 0.561 8.006 28409 Z= 0.301 Chirality : 0.044 0.214 3122 Planarity : 0.005 0.053 3415 Dihedral : 14.506 166.119 3798 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.90 % Allowed : 13.83 % Favored : 83.27 % 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: 0.71 (0.17), residues: 2302 helix: 1.44 (0.20), residues: 641 sheet: 0.16 (0.24), residues: 403 loop : 0.17 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1214 TYR 0.016 0.002 TYR D 786 PHE 0.016 0.002 PHE D1147 TRP 0.020 0.001 TRP D 429 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (20708) covalent geometry : angle 0.55932 / 0.30 (28403) hydrogen bonds : bond 0.04970 / 5.19 ( 806) hydrogen bonds : angle 4.85783 / 5.48 ( 2169) metal coordination : bond 0.00216 / 0.19 ( 4) metal coordination : angle 3.02958 / 5.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 141 GLN cc_start: 0.7526 (tp40) cc_final: 0.7320 (tm-30) REVERT: B 259 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7230 (tptt) REVERT: B 262 LYS cc_start: 0.7283 (mtpt) cc_final: 0.6925 (ttpt) REVERT: B 265 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: B 326 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5738 (pttp) REVERT: B 370 ARG cc_start: 0.7804 (tpt-90) cc_final: 0.6887 (ttp-170) REVERT: B 371 GLU cc_start: 0.7890 (pt0) cc_final: 0.7642 (pt0) REVERT: B 412 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7754 (mtt-85) REVERT: B 423 ASN cc_start: 0.8162 (m110) cc_final: 0.7952 (t0) REVERT: B 425 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8295 (mmtm) REVERT: B 450 LYS cc_start: 0.8721 (mttm) cc_final: 0.8290 (tptp) REVERT: B 454 LYS cc_start: 0.8859 (tttt) cc_final: 0.8635 (tttp) REVERT: B 484 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8088 (mt-10) REVERT: B 523 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6401 (tp30) REVERT: B 526 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: C 93 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8246 (m) REVERT: C 136 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8693 (mtt) REVERT: C 181 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8463 (ttmm) REVERT: C 323 GLU cc_start: 0.8082 (tp30) cc_final: 0.7765 (tp30) REVERT: C 367 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: C 414 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6800 (mtm110) REVERT: C 427 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6875 (mp-120) REVERT: C 559 GLN cc_start: 0.7727 (tt0) cc_final: 0.7285 (tt0) REVERT: C 560 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7474 (ttp80) REVERT: C 572 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7759 (tp) REVERT: C 583 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: C 584 SER cc_start: 0.8034 (p) cc_final: 0.7735 (t) REVERT: D 7 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7335 (mtpp) REVERT: D 47 ASP cc_start: 0.6138 (m-30) cc_final: 0.5548 (t70) REVERT: D 102 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7068 (tp30) REVERT: D 194 THR cc_start: 0.8449 (m) cc_final: 0.8117 (p) REVERT: D 232 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: D 407 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: D 412 LYS cc_start: 0.8869 (mtpm) cc_final: 0.8598 (mmmt) REVERT: D 422 GLN cc_start: 0.6683 (mm110) cc_final: 0.6170 (tt0) REVERT: D 541 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7658 (mmtt) REVERT: D 596 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8404 (mtmt) REVERT: D 666 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7268 (mmm) REVERT: D 669 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7445 (t0) REVERT: D 685 MET cc_start: 0.5586 (tpp) cc_final: 0.5207 (tpt) REVERT: D 836 ARG cc_start: 0.7331 (mtt90) cc_final: 0.6830 (mtp180) REVERT: D 844 ASP cc_start: 0.8112 (t0) cc_final: 0.7882 (t70) REVERT: D 852 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: D 853 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (pt) REVERT: D 931 ASP cc_start: 0.8151 (m-30) cc_final: 0.7781 (t0) REVERT: D 1097 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5712 (pt0) REVERT: D 1199 ASP cc_start: 0.7521 (m-30) cc_final: 0.6882 (m-30) outliers start: 57 outliers final: 24 residues processed: 275 average time/residue: 0.6830 time to fit residues: 209.8322 Evaluate side-chains 274 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 164 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 195 ASN D 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133858 restraints weight = 19531.121| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.58 r_work: 0.3074 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20712 Z= 0.145 Angle : 0.552 7.754 28409 Z= 0.297 Chirality : 0.043 0.216 3122 Planarity : 0.004 0.053 3415 Dihedral : 14.500 166.746 3796 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.20 % Allowed : 13.88 % Favored : 82.92 % 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: 0.73 (0.17), residues: 2302 helix: 1.48 (0.20), residues: 641 sheet: 0.18 (0.25), residues: 403 loop : 0.16 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1214 TYR 0.016 0.002 TYR D 786 PHE 0.015 0.002 PHE D1147 TRP 0.021 0.001 TRP D 429 HIS 0.007 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (20708) covalent geometry : angle 0.54984 / 0.30 (28403) hydrogen bonds : bond 0.04862 / 5.08 ( 806) hydrogen bonds : angle 4.83009 / 5.45 ( 2169) metal coordination : bond 0.00253 / 0.23 ( 4) metal coordination : angle 3.06647 / 5.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.951 Fit side-chains REVERT: B 8 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: B 141 GLN cc_start: 0.7572 (tp40) cc_final: 0.7266 (tm-30) REVERT: B 259 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7246 (tptt) REVERT: B 262 LYS cc_start: 0.7326 (mtpt) cc_final: 0.6940 (ptpt) REVERT: B 265 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: B 326 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5731 (pttp) REVERT: B 370 ARG cc_start: 0.7794 (tpt-90) cc_final: 0.6877 (ttp-170) REVERT: B 412 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7741 (mtt-85) REVERT: B 423 ASN cc_start: 0.8166 (m110) cc_final: 0.7954 (t0) REVERT: B 425 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8304 (mmtm) REVERT: B 450 LYS cc_start: 0.8731 (mttm) cc_final: 0.8302 (tptp) REVERT: B 454 LYS cc_start: 0.8870 (tttt) cc_final: 0.8654 (tttp) REVERT: B 484 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 523 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6420 (tp30) REVERT: B 526 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: C 70 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5690 (mmt) REVERT: C 93 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (m) REVERT: C 136 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8721 (mtt) REVERT: C 181 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8450 (ttmm) REVERT: C 323 GLU cc_start: 0.8079 (tp30) cc_final: 0.7758 (tp30) REVERT: C 367 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: C 414 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6867 (mtm110) REVERT: C 427 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6823 (mp-120) REVERT: C 559 GLN cc_start: 0.7765 (tt0) cc_final: 0.7341 (tt0) REVERT: C 560 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7549 (ttp80) REVERT: C 572 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7772 (tp) REVERT: C 584 SER cc_start: 0.8036 (p) cc_final: 0.7732 (t) REVERT: D 7 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7348 (mtpp) REVERT: D 47 ASP cc_start: 0.6136 (m-30) cc_final: 0.5544 (t70) REVERT: D 102 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7106 (tp30) REVERT: D 194 THR cc_start: 0.8438 (m) cc_final: 0.8160 (p) REVERT: D 232 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6204 (tm-30) REVERT: D 407 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8241 (tp30) REVERT: D 412 LYS cc_start: 0.8893 (mtpm) cc_final: 0.8616 (mmmt) REVERT: D 422 GLN cc_start: 0.6631 (mm110) cc_final: 0.6156 (tt0) REVERT: D 541 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7650 (mmtt) REVERT: D 596 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8405 (mtmt) REVERT: D 666 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7291 (mmm) REVERT: D 669 ASN cc_start: 0.7827 (t0) cc_final: 0.7496 (t0) REVERT: D 795 LEU cc_start: 0.8786 (mp) cc_final: 0.8332 (mp) REVERT: D 836 ARG cc_start: 0.7338 (mtt90) cc_final: 0.6841 (mtp180) REVERT: D 844 ASP cc_start: 0.8108 (t0) cc_final: 0.7886 (t70) REVERT: D 852 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: D 853 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8257 (pt) REVERT: D 931 ASP cc_start: 0.8172 (m-30) cc_final: 0.7812 (t0) REVERT: D 1087 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: D 1097 GLU cc_start: 0.6506 (mt-10) cc_final: 0.5736 (pt0) REVERT: D 1199 ASP cc_start: 0.7652 (m-30) cc_final: 0.7052 (m-30) outliers start: 63 outliers final: 28 residues processed: 273 average time/residue: 0.7215 time to fit residues: 220.4172 Evaluate side-chains 281 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 852 GLU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 1087 GLN Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 141 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 195 ASN D 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135284 restraints weight = 19389.095| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.57 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20712 Z= 0.110 Angle : 0.506 7.319 28409 Z= 0.275 Chirality : 0.042 0.212 3122 Planarity : 0.004 0.053 3415 Dihedral : 14.467 169.774 3796 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.64 % Allowed : 14.69 % Favored : 82.66 % 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: 0.88 (0.17), residues: 2302 helix: 1.67 (0.20), residues: 641 sheet: 0.28 (0.25), residues: 407 loop : 0.22 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1214 TYR 0.014 0.001 TYR D 786 PHE 0.013 0.001 PHE C 155 TRP 0.022 0.001 TRP D 429 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (20708) covalent geometry : angle 0.50444 / 0.27 (28403) hydrogen bonds : bond 0.04332 / 4.55 ( 806) hydrogen bonds : angle 4.68316 / 5.30 ( 2169) metal coordination : bond 0.00268 / 0.24 ( 4) metal coordination : angle 2.72617 / 5.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.444 Fit side-chains REVERT: B 8 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 123 SER cc_start: 0.8288 (p) cc_final: 0.8064 (m) REVERT: B 141 GLN cc_start: 0.7587 (tp40) cc_final: 0.7317 (tm-30) REVERT: B 259 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7247 (tptt) REVERT: B 262 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6938 (ptpt) REVERT: B 265 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: B 326 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5692 (pttp) REVERT: B 370 ARG cc_start: 0.7676 (tpt-90) cc_final: 0.6821 (ttp-170) REVERT: B 421 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7267 (pt) REVERT: B 425 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8335 (mmtm) REVERT: B 450 LYS cc_start: 0.8692 (mttm) cc_final: 0.8215 (mmpt) REVERT: B 454 LYS cc_start: 0.8842 (tttt) cc_final: 0.8619 (tttp) REVERT: B 484 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 523 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6411 (tp30) REVERT: B 526 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: C 70 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5637 (mmt) REVERT: C 93 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (m) REVERT: C 136 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8724 (mtt) REVERT: C 323 GLU cc_start: 0.7978 (tp30) cc_final: 0.7688 (tp30) REVERT: C 367 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: C 503 ASN cc_start: 0.8091 (m-40) cc_final: 0.7776 (t0) REVERT: C 559 GLN cc_start: 0.7756 (tt0) cc_final: 0.7400 (tt0) REVERT: C 560 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7571 (ttp80) REVERT: C 572 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7764 (tp) REVERT: C 584 SER cc_start: 0.8071 (p) cc_final: 0.7756 (t) REVERT: D 7 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7294 (mtpp) REVERT: D 47 ASP cc_start: 0.6162 (m-30) cc_final: 0.5607 (t70) REVERT: D 50 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7804 (mm110) REVERT: D 102 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7161 (tp30) REVERT: D 194 THR cc_start: 0.8544 (m) cc_final: 0.8302 (p) REVERT: D 327 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7986 (mt-10) REVERT: D 407 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: D 412 LYS cc_start: 0.8812 (mtpm) cc_final: 0.8572 (mmmt) REVERT: D 422 GLN cc_start: 0.6597 (mm110) cc_final: 0.6189 (tt0) REVERT: D 596 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8406 (mtmt) REVERT: D 666 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7358 (mmm) REVERT: D 669 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7438 (t0) REVERT: D 685 MET cc_start: 0.5933 (tpp) cc_final: 0.5534 (tpt) REVERT: D 795 LEU cc_start: 0.8751 (mp) cc_final: 0.8246 (mp) REVERT: D 836 ARG cc_start: 0.7325 (mtt90) cc_final: 0.6862 (mtp180) REVERT: D 853 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8185 (pt) REVERT: D 931 ASP cc_start: 0.8109 (m-30) cc_final: 0.7827 (t0) REVERT: D 1097 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5568 (pt0) REVERT: D 1199 ASP cc_start: 0.7732 (m-30) cc_final: 0.7158 (m-30) outliers start: 52 outliers final: 22 residues processed: 279 average time/residue: 0.6394 time to fit residues: 199.1953 Evaluate side-chains 273 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 198 optimal weight: 5.9990 chunk 234 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.132616 restraints weight = 19343.882| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.55 r_work: 0.3060 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20712 Z= 0.218 Angle : 0.626 7.356 28409 Z= 0.333 Chirality : 0.047 0.211 3122 Planarity : 0.005 0.053 3415 Dihedral : 14.464 163.869 3796 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.39 % Allowed : 15.46 % Favored : 82.16 % 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: 0.58 (0.17), residues: 2302 helix: 1.29 (0.20), residues: 648 sheet: 0.12 (0.24), residues: 414 loop : 0.10 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.025 0.002 TYR D1156 PHE 0.018 0.002 PHE B 127 TRP 0.021 0.002 TRP D 429 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (20708) covalent geometry : angle 0.62467 / 0.33 (28403) hydrogen bonds : bond 0.05628 / 5.87 ( 806) hydrogen bonds : angle 4.96487 / 5.61 ( 2169) metal coordination : bond 0.00201 / 0.17 ( 4) metal coordination : angle 3.13883 / 6.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.470 Fit side-chains REVERT: B 8 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: B 141 GLN cc_start: 0.7622 (tp40) cc_final: 0.7347 (tm-30) REVERT: B 205 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8659 (p0) REVERT: B 259 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7371 (tptt) REVERT: B 262 LYS cc_start: 0.7330 (mtpt) cc_final: 0.6955 (ttpt) REVERT: B 326 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5873 (pttp) REVERT: B 370 ARG cc_start: 0.7765 (tpt-90) cc_final: 0.6889 (ttp-170) REVERT: B 412 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7911 (mtt-85) REVERT: B 425 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8357 (mmtm) REVERT: B 450 LYS cc_start: 0.8751 (mttm) cc_final: 0.8470 (mtpt) REVERT: B 454 LYS cc_start: 0.8897 (tttt) cc_final: 0.8663 (tttp) REVERT: B 484 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8042 (mt-10) REVERT: B 523 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6719 (tp30) REVERT: B 526 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: C 70 MET cc_start: 0.6074 (mmp) cc_final: 0.5796 (mmt) REVERT: C 93 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8285 (m) REVERT: C 136 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8680 (mtt) REVERT: C 323 GLU cc_start: 0.7990 (tp30) cc_final: 0.7676 (tp30) REVERT: C 343 GLU cc_start: 0.7645 (mp0) cc_final: 0.7333 (pm20) REVERT: C 367 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: C 503 ASN cc_start: 0.8088 (m-40) cc_final: 0.7760 (t0) REVERT: C 559 GLN cc_start: 0.7853 (tt0) cc_final: 0.7446 (tt0) REVERT: C 560 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7630 (ttp80) REVERT: C 572 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7854 (tp) REVERT: D 7 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7435 (mtpp) REVERT: D 47 ASP cc_start: 0.6209 (m-30) cc_final: 0.5644 (t70) REVERT: D 102 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7129 (tp30) REVERT: D 194 THR cc_start: 0.8477 (m) cc_final: 0.8238 (p) REVERT: D 407 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: D 412 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8599 (mmmt) REVERT: D 422 GLN cc_start: 0.6751 (mm110) cc_final: 0.6284 (tt0) REVERT: D 666 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: D 669 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7491 (t0) REVERT: D 739 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7016 (tttp) REVERT: D 795 LEU cc_start: 0.8839 (mp) cc_final: 0.8337 (mp) REVERT: D 836 ARG cc_start: 0.7356 (mtt90) cc_final: 0.6874 (mtp180) REVERT: D 853 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8334 (pt) REVERT: D 931 ASP cc_start: 0.8148 (m-30) cc_final: 0.7836 (t0) REVERT: D 1082 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: D 1097 GLU cc_start: 0.6486 (mt-10) cc_final: 0.5779 (pt0) REVERT: D 1199 ASP cc_start: 0.7683 (m-30) cc_final: 0.7125 (m-30) outliers start: 47 outliers final: 22 residues processed: 262 average time/residue: 0.6555 time to fit residues: 191.6724 Evaluate side-chains 260 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 739 LYS Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 35 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 169 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 117 optimal weight: 0.0470 chunk 218 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN C 263 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 195 ASN D 392 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.166338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136918 restraints weight = 19615.532| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.57 r_work: 0.3141 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20712 Z= 0.095 Angle : 0.496 7.707 28409 Z= 0.270 Chirality : 0.041 0.212 3122 Planarity : 0.004 0.053 3415 Dihedral : 14.482 170.500 3796 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 16.68 % Favored : 81.85 % 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: 0.88 (0.17), residues: 2302 helix: 1.69 (0.20), residues: 648 sheet: 0.26 (0.25), residues: 402 loop : 0.21 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1214 TYR 0.023 0.001 TYR D1156 PHE 0.019 0.001 PHE B 127 TRP 0.026 0.001 TRP D 429 HIS 0.006 0.001 HIS D 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (20708) covalent geometry : angle 0.49437 / 0.27 (28403) hydrogen bonds : bond 0.04107 / 4.34 ( 806) hydrogen bonds : angle 4.64299 / 5.24 ( 2169) metal coordination : bond 0.00384 / 0.35 ( 4) metal coordination : angle 2.49978 / 4.71 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.762 Fit side-chains REVERT: B 8 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: B 141 GLN cc_start: 0.7558 (tp40) cc_final: 0.7268 (tm-30) REVERT: B 259 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7187 (tptt) REVERT: B 262 LYS cc_start: 0.7318 (mtpt) cc_final: 0.6940 (ttpt) REVERT: B 326 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5613 (pttp) REVERT: B 370 ARG cc_start: 0.7612 (tpt-90) cc_final: 0.6752 (ttp-170) REVERT: B 425 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (mmtm) REVERT: B 450 LYS cc_start: 0.8701 (mttm) cc_final: 0.8246 (mmtt) REVERT: B 454 LYS cc_start: 0.8840 (tttt) cc_final: 0.8637 (tttp) REVERT: B 484 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 523 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6381 (tp30) REVERT: C 70 MET cc_start: 0.5915 (mmp) cc_final: 0.5549 (mmt) REVERT: C 93 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8226 (m) REVERT: C 136 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: C 323 GLU cc_start: 0.7906 (tp30) cc_final: 0.7601 (tp30) REVERT: C 343 GLU cc_start: 0.7645 (mp0) cc_final: 0.7383 (pm20) REVERT: C 367 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: C 414 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6844 (mtm110) REVERT: C 503 ASN cc_start: 0.8112 (m-40) cc_final: 0.7775 (t0) REVERT: C 555 MET cc_start: 0.8464 (tpp) cc_final: 0.8237 (mmm) REVERT: C 559 GLN cc_start: 0.7752 (tt0) cc_final: 0.7469 (tt0) REVERT: C 560 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7576 (ttp80) REVERT: D 47 ASP cc_start: 0.6186 (m-30) cc_final: 0.5635 (t70) REVERT: D 50 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7730 (mm-40) REVERT: D 102 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7054 (tp30) REVERT: D 194 THR cc_start: 0.8510 (m) cc_final: 0.8272 (p) REVERT: D 327 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7946 (mt-10) REVERT: D 407 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: D 412 LYS cc_start: 0.8820 (mtpm) cc_final: 0.8574 (mmmt) REVERT: D 422 GLN cc_start: 0.6537 (mm110) cc_final: 0.6147 (tt0) REVERT: D 666 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7301 (mmm) REVERT: D 669 ASN cc_start: 0.7749 (t0) cc_final: 0.7460 (t0) REVERT: D 685 MET cc_start: 0.5740 (tpp) cc_final: 0.5455 (tpt) REVERT: D 795 LEU cc_start: 0.8705 (mp) cc_final: 0.8240 (mp) REVERT: D 836 ARG cc_start: 0.7332 (mtt90) cc_final: 0.6832 (mtp180) REVERT: D 931 ASP cc_start: 0.8120 (m-30) cc_final: 0.7810 (t0) REVERT: D 1082 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: D 1097 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5530 (pt0) REVERT: D 1199 ASP cc_start: 0.7762 (m-30) cc_final: 0.7142 (m-30) outliers start: 29 outliers final: 12 residues processed: 256 average time/residue: 0.6434 time to fit residues: 183.8258 Evaluate side-chains 249 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 856 SER Chi-restraints excluded: chain D residue 1082 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN C 263 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134498 restraints weight = 19667.842| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.48 r_work: 0.3077 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20712 Z= 0.175 Angle : 0.577 7.812 28409 Z= 0.308 Chirality : 0.045 0.218 3122 Planarity : 0.005 0.053 3415 Dihedral : 14.412 166.953 3796 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.47 % Allowed : 16.78 % Favored : 81.75 % 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: 0.76 (0.17), residues: 2302 helix: 1.51 (0.20), residues: 647 sheet: 0.25 (0.25), residues: 404 loop : 0.15 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 422 TYR 0.027 0.002 TYR D1156 PHE 0.018 0.002 PHE B 127 TRP 0.018 0.002 TRP D 429 HIS 0.007 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (20708) covalent geometry : angle 0.57487 / 0.31 (28403) hydrogen bonds : bond 0.05052 / 5.28 ( 806) hydrogen bonds : angle 4.82858 / 5.47 ( 2169) metal coordination : bond 0.00210 / 0.18 ( 4) metal coordination : angle 3.21376 / 6.26 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6655.04 seconds wall clock time: 114 minutes 1.00 seconds (6841.00 seconds total)