Starting phenix.real_space_refine on Mon Aug 25 04:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.map" model { file = "/net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cll_16717/08_2025/8cll_16717.cif" } resolution = 3.4 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= 0.006 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 164 5.16 5 C 16150 2.51 5 N 4418 2.21 5 O 4490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25226 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "B" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5496 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 653} Chain breaks: 2 Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4601 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 534} Chain breaks: 1 Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5496 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 653} Chain breaks: 2 Chain: "H" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4601 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 534} Chain breaks: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7735 SG CYS B 788 46.027 71.017 193.545 1.00136.96 S ATOM 7946 SG CYS B 814 43.778 70.655 195.239 1.00147.83 S ATOM 7970 SG CYS B 817 45.511 73.585 194.267 1.00143.68 S ATOM 7396 SG CYS B 747 51.101 54.207 211.937 1.00220.65 S ATOM 7416 SG CYS B 750 53.312 52.131 214.131 1.00223.84 S ATOM 7530 SG CYS B 764 53.738 56.069 214.244 1.00223.21 S ATOM 20007 SG CYS G 747 72.488 100.730 31.075 1.00213.20 S ATOM 20027 SG CYS G 750 74.590 100.422 28.018 1.00221.15 S ATOM 20141 SG CYS G 764 71.171 101.753 27.648 1.00222.55 S ATOM 20346 SG CYS G 788 54.142 93.316 47.252 1.00137.47 S ATOM 20557 SG CYS G 814 53.321 97.170 46.227 1.00130.31 S ATOM 20581 SG CYS G 817 51.369 94.087 46.694 1.00134.83 S Time building chain proxies: 6.07, per 1000 atoms: 0.24 Number of scatterers: 25226 At special positions: 0 Unit cell: (107.682, 134.808, 230.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 164 16.00 O 4490 8.00 N 4418 7.00 C 16150 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 814 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 817 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 788 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 768 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 750 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 747 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 764 " pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" ND1 HIS G 768 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 750 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 764 " pdb="ZN ZN G 901 " - pdb=" SG CYS G 747 " pdb=" ZN G 902 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 814 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 788 " pdb="ZN ZN G 902 " - pdb=" SG CYS G 817 " Number of angles added : 6 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 41 sheets defined 28.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.722A pdb=" N GLU A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 174 through 187 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 205 through 219 removed outlier: 4.159A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.525A pdb=" N GLU B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 517 through 527 Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.654A pdb=" N LEU B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.675A pdb=" N TRP B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 698 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 724 through 738 Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'C' and resid 300 through 322 Proline residue: C 306 - end of helix removed outlier: 3.793A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS C 312 " --> pdb=" O TRP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.524A pdb=" N LEU C 519 " --> pdb=" O HIS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 746 through 749 Processing helix chain 'C' and resid 786 through 792 Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.650A pdb=" N GLU C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 889 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.640A pdb=" N GLU F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 40 through 54 removed outlier: 4.093A pdb=" N PHE F 46 " --> pdb=" O CYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 174 through 188 removed outlier: 3.558A pdb=" N ARG F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 205 through 219 removed outlier: 4.121A pdb=" N ILE F 215 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU F 216 " --> pdb=" O HIS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 396 through 410 Processing helix chain 'G' and resid 122 through 136 Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'G' and resid 208 through 218 Processing helix chain 'G' and resid 235 through 245 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 468 through 473 Processing helix chain 'G' and resid 517 through 527 Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 551 removed outlier: 3.847A pdb=" N LEU G 542 " --> pdb=" O ASP G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 568 Processing helix chain 'G' and resid 570 through 588 removed outlier: 3.635A pdb=" N TRP G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 664 through 698 Processing helix chain 'G' and resid 708 through 719 Processing helix chain 'G' and resid 720 through 723 Processing helix chain 'G' and resid 724 through 738 Processing helix chain 'G' and resid 765 through 767 No H-bonds generated for 'chain 'G' and resid 765 through 767' Processing helix chain 'G' and resid 803 through 810 Processing helix chain 'H' and resid 300 through 322 Proline residue: H 306 - end of helix removed outlier: 3.684A pdb=" N HIS H 312 " --> pdb=" O TRP H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 331 removed outlier: 3.985A pdb=" N ILE H 331 " --> pdb=" O ALA H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 335 No H-bonds generated for 'chain 'H' and resid 333 through 335' Processing helix chain 'H' and resid 341 through 346 Processing helix chain 'H' and resid 515 through 523 Processing helix chain 'H' and resid 676 through 679 Processing helix chain 'H' and resid 740 through 744 Processing helix chain 'H' and resid 746 through 749 Processing helix chain 'H' and resid 786 through 792 Processing helix chain 'H' and resid 808 through 811 Processing helix chain 'H' and resid 812 through 822 Processing helix chain 'H' and resid 867 through 870 Processing helix chain 'H' and resid 871 through 889 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.396A pdb=" N GLY A 112 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 193 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.216A pdb=" N GLY B 479 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR B 494 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR B 477 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.133A pdb=" N VAL B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.851A pdb=" N LEU B 185 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 167 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 183 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 191 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP B 207 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 193 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.646A pdb=" N LEU B 279 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 251 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 277 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 253 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 275 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 255 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER B 273 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 302 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN B 291 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE B 300 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.722A pdb=" N GLY B 334 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 316 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 332 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 330 " --> pdb=" O TRP B 318 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 320 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 328 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS B 327 " --> pdb=" O PHE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.722A pdb=" N GLY B 334 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 316 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 332 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 330 " --> pdb=" O TRP B 318 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 320 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 328 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 340 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 371 through 381 removed outlier: 3.755A pdb=" N SER B 373 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER B 387 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 406 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 399 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.684A pdb=" N SER B 428 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 447 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB5, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 340 removed outlier: 4.648A pdb=" N ILE C 532 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C 535 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE C 459 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY C 443 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 461 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU C 438 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 358 through 362 removed outlier: 5.988A pdb=" N ARG C 751 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 733 " --> pdb=" O ARG C 751 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 731 " --> pdb=" O PRO C 753 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 755 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 719 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 710 " --> pdb=" O GLY C 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 389 through 392 Processing sheet with id=AB9, first strand: chain 'C' and resid 470 through 475 removed outlier: 6.570A pdb=" N ALA C 502 " --> pdb=" O TRP C 471 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU C 473 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA C 500 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 475 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 498 " --> pdb=" O PHE C 475 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 513 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 498 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE C 511 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 500 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 509 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 557 through 562 removed outlier: 3.715A pdb=" N SER C 559 " --> pdb=" O GLY C 574 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 607 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 621 removed outlier: 3.827A pdb=" N GLY C 633 " --> pdb=" O LYS C 637 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 651 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 658 through 662 removed outlier: 3.797A pdb=" N GLU C 660 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 674 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY C 685 " --> pdb=" O GLN C 674 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR C 688 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N PHE C 700 " --> pdb=" O TYR C 688 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 121 through 122 Processing sheet with id=AC5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.346A pdb=" N GLY F 112 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 222 through 230 Processing sheet with id=AC7, first strand: chain 'F' and resid 384 through 385 Processing sheet with id=AC8, first strand: chain 'G' and resid 53 through 59 removed outlier: 5.017A pdb=" N PHE G 512 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 510 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR G 488 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL G 482 " --> pdb=" O TYR G 488 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA G 490 " --> pdb=" O ILE G 480 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE G 480 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 492 " --> pdb=" O HIS G 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 70 through 72 removed outlier: 4.298A pdb=" N VAL G 103 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 164 through 169 removed outlier: 7.184A pdb=" N LEU G 191 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP G 207 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE G 193 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 248 through 257 removed outlier: 5.848A pdb=" N MET G 251 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU G 279 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP G 253 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA G 277 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY G 255 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU G 275 " --> pdb=" O GLY G 255 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN G 284 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN G 291 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE G 300 " --> pdb=" O GLN G 291 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 313 through 323 removed outlier: 6.077A pdb=" N ILE G 340 " --> pdb=" O LEU G 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 360 " --> pdb=" O ILE G 342 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 371 through 381 removed outlier: 3.787A pdb=" N SER G 373 " --> pdb=" O ALA G 394 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS G 386 " --> pdb=" O HIS G 381 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER G 387 " --> pdb=" O ILE G 406 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE G 406 " --> pdb=" O SER G 387 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 399 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 428 through 431 removed outlier: 3.648A pdb=" N SER G 428 " --> pdb=" O CYS G 441 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL G 447 " --> pdb=" O ILE G 466 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 761 through 763 Processing sheet with id=AD7, first strand: chain 'G' and resid 786 through 787 Processing sheet with id=AD8, first strand: chain 'H' and resid 337 through 339 removed outlier: 4.759A pdb=" N VAL H 535 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE H 459 " --> pdb=" O GLY H 443 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY H 443 " --> pdb=" O PHE H 459 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR H 461 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 438 " --> pdb=" O SER H 419 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER H 419 " --> pdb=" O LEU H 438 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR H 414 " --> pdb=" O TRP H 402 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP H 402 " --> pdb=" O TYR H 414 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 416 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU H 400 " --> pdb=" O ALA H 416 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE H 418 " --> pdb=" O TRP H 398 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 358 through 362 removed outlier: 6.460A pdb=" N SER H 359 " --> pdb=" O PHE H 798 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP H 800 " --> pdb=" O SER H 359 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN H 361 " --> pdb=" O ASP H 800 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG H 751 " --> pdb=" O ILE H 733 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE H 733 " --> pdb=" O ARG H 751 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA H 731 " --> pdb=" O PRO H 753 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 728 " --> pdb=" O ASP H 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 719 " --> pdb=" O GLY H 713 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY H 713 " --> pdb=" O THR H 719 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA H 721 " --> pdb=" O LEU H 711 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU H 711 " --> pdb=" O ALA H 721 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY H 723 " --> pdb=" O TRP H 709 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 378 through 379 removed outlier: 4.051A pdb=" N SER H 378 " --> pdb=" O PHE H 392 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU H 860 " --> pdb=" O GLY H 856 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY H 856 " --> pdb=" O LEU H 860 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 470 through 475 removed outlier: 6.647A pdb=" N ALA H 502 " --> pdb=" O TRP H 471 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU H 473 " --> pdb=" O ALA H 500 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA H 500 " --> pdb=" O LEU H 473 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE H 475 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU H 498 " --> pdb=" O PHE H 475 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 513 " --> pdb=" O LEU H 496 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU H 498 " --> pdb=" O PHE H 511 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE H 511 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA H 500 " --> pdb=" O LEU H 509 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU H 509 " --> pdb=" O ALA H 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 557 through 562 removed outlier: 6.298A pdb=" N GLY H 574 " --> pdb=" O LEU H 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU H 560 " --> pdb=" O ALA H 572 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA H 572 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP H 562 " --> pdb=" O HIS H 570 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS H 570 " --> pdb=" O TRP H 562 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET H 579 " --> pdb=" O TYR H 575 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN H 607 " --> pdb=" O PHE H 582 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 618 through 621 removed outlier: 3.634A pdb=" N ALA H 632 " --> pdb=" O THR H 618 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 651 " --> pdb=" O PHE H 640 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 658 through 662 removed outlier: 3.763A pdb=" N GLU H 660 " --> pdb=" O ALA H 673 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN H 674 " --> pdb=" O GLY H 685 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY H 685 " --> pdb=" O GLN H 674 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR H 688 " --> pdb=" O PHE H 700 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE H 700 " --> pdb=" O TYR H 688 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8210 1.35 - 1.47: 6388 1.47 - 1.60: 11042 1.60 - 1.72: 0 1.72 - 1.85: 238 Bond restraints: 25878 Sorted by residual: bond pdb=" CB CYS G 817 " pdb=" SG CYS G 817 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG1 ILE H 720 " pdb=" CD1 ILE H 720 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.42e-01 bond pdb=" CA GLU G 68 " pdb=" C GLU G 68 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.26e-02 6.30e+03 8.41e-01 bond pdb=" CB ILE A 163 " pdb=" CG2 ILE A 163 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.42e-01 bond pdb=" CB VAL H 581 " pdb=" CG1 VAL H 581 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.15e-01 ... (remaining 25873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 34103 1.72 - 3.45: 883 3.45 - 5.17: 109 5.17 - 6.89: 10 6.89 - 8.61: 1 Bond angle restraints: 35106 Sorted by residual: angle pdb=" N GLY B 338 " pdb=" CA GLY B 338 " pdb=" C GLY B 338 " ideal model delta sigma weight residual 112.34 120.95 -8.61 2.04e+00 2.40e-01 1.78e+01 angle pdb=" N ASP G 75 " pdb=" CA ASP G 75 " pdb=" C ASP G 75 " ideal model delta sigma weight residual 112.54 108.01 4.53 1.51e+00 4.39e-01 9.01e+00 angle pdb=" C CYS G 817 " pdb=" N ASP G 818 " pdb=" CA ASP G 818 " ideal model delta sigma weight residual 122.31 117.04 5.27 1.81e+00 3.05e-01 8.47e+00 angle pdb=" N ALA H 346 " pdb=" CA ALA H 346 " pdb=" C ALA H 346 " ideal model delta sigma weight residual 109.81 116.13 -6.32 2.21e+00 2.05e-01 8.19e+00 angle pdb=" CA GLN G 358 " pdb=" CB GLN G 358 " pdb=" CG GLN G 358 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 ... (remaining 35101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14430 17.98 - 35.95: 892 35.95 - 53.93: 124 53.93 - 71.90: 44 71.90 - 89.88: 26 Dihedral angle restraints: 15516 sinusoidal: 6368 harmonic: 9148 Sorted by residual: dihedral pdb=" CA LEU G 775 " pdb=" C LEU G 775 " pdb=" N THR G 776 " pdb=" CA THR G 776 " ideal model delta harmonic sigma weight residual 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LYS G 760 " pdb=" C LYS G 760 " pdb=" N GLN G 761 " pdb=" CA GLN G 761 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU G 459 " pdb=" C LEU G 459 " pdb=" N LYS G 460 " pdb=" CA LYS G 460 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 15513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2319 0.036 - 0.071: 1012 0.071 - 0.107: 348 0.107 - 0.142: 141 0.142 - 0.178: 14 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CB VAL H 866 " pdb=" CA VAL H 866 " pdb=" CG1 VAL H 866 " pdb=" CG2 VAL H 866 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA TYR B 777 " pdb=" N TYR B 777 " pdb=" C TYR B 777 " pdb=" CB TYR B 777 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ARG H 636 " pdb=" N ARG H 636 " pdb=" C ARG H 636 " pdb=" CB ARG H 636 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 3831 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 796 " 0.304 9.50e-02 1.11e+02 1.37e-01 1.47e+01 pdb=" NE ARG G 796 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG G 796 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG G 796 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 796 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " -0.254 9.50e-02 1.11e+02 1.15e-01 1.03e+01 pdb=" NE ARG B 796 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 796 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B 796 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 186 " -0.249 9.50e-02 1.11e+02 1.12e-01 9.76e+00 pdb=" NE ARG F 186 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 186 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG F 186 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 186 " -0.001 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 127 2.57 - 3.15: 20539 3.15 - 3.73: 38499 3.73 - 4.32: 56095 4.32 - 4.90: 93429 Nonbonded interactions: 208689 Sorted by model distance: nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 901 " model vdw 1.984 2.230 nonbonded pdb=" OD1 ASP G 792 " pdb="ZN ZN G 902 " model vdw 1.998 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 901 " model vdw 2.000 2.230 nonbonded pdb=" OD2 ASP G 792 " pdb="ZN ZN G 902 " model vdw 2.004 2.230 nonbonded pdb=" OG SER B 793 " pdb="ZN ZN B 901 " model vdw 2.084 2.230 ... (remaining 208684 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 26.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25892 Z= 0.134 Angle : 0.666 8.615 35112 Z= 0.371 Chirality : 0.047 0.178 3834 Planarity : 0.009 0.137 4494 Dihedral : 12.967 89.880 9600 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: -0.75 (0.14), residues: 3120 helix: -0.76 (0.15), residues: 790 sheet: 0.05 (0.18), residues: 784 loop : -0.52 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.004 ARG G 796 TYR 0.028 0.004 TYR A 98 PHE 0.014 0.002 PHE H 391 TRP 0.038 0.002 TRP H 481 HIS 0.008 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00309 (25878) covalent geometry : angle 0.66280 (35106) hydrogen bonds : bond 0.18188 ( 971) hydrogen bonds : angle 7.69002 ( 2754) metal coordination : bond 0.02165 ( 14) metal coordination : angle 4.96036 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8589 (tmm) cc_final: 0.8272 (ptm) REVERT: B 174 CYS cc_start: 0.8612 (m) cc_final: 0.8074 (m) REVERT: B 406 ILE cc_start: 0.7977 (mt) cc_final: 0.7553 (mt) REVERT: B 681 MET cc_start: 0.9304 (tpt) cc_final: 0.8816 (tpp) REVERT: B 685 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8508 (tpp80) REVERT: B 715 PHE cc_start: 0.8522 (t80) cc_final: 0.8151 (t80) REVERT: B 783 LEU cc_start: 0.8660 (mt) cc_final: 0.8364 (mt) REVERT: C 387 TRP cc_start: 0.7898 (m-10) cc_final: 0.7316 (m-10) REVERT: C 563 MET cc_start: 0.8727 (ttt) cc_final: 0.8510 (ttm) REVERT: C 683 LEU cc_start: 0.7368 (mt) cc_final: 0.7050 (mm) REVERT: C 737 MET cc_start: 0.8956 (mmt) cc_final: 0.8597 (mmt) REVERT: C 888 MET cc_start: 0.8351 (ttm) cc_final: 0.7956 (ttm) REVERT: F 116 TYR cc_start: 0.8492 (m-80) cc_final: 0.7932 (m-10) REVERT: F 178 TYR cc_start: 0.7728 (t80) cc_final: 0.7493 (t80) REVERT: F 211 TYR cc_start: 0.8833 (t80) cc_final: 0.8506 (t80) REVERT: G 200 LEU cc_start: 0.8388 (mp) cc_final: 0.8143 (tp) REVERT: G 696 TYR cc_start: 0.9296 (t80) cc_final: 0.8720 (t80) REVERT: G 743 PHE cc_start: 0.8407 (m-80) cc_final: 0.8012 (m-80) REVERT: G 771 LEU cc_start: 0.8678 (mt) cc_final: 0.8402 (mm) REVERT: H 489 LYS cc_start: 0.7513 (mmmt) cc_final: 0.6945 (pttt) REVERT: H 563 MET cc_start: 0.8920 (ttt) cc_final: 0.8665 (ttt) REVERT: H 720 ILE cc_start: 0.9060 (mt) cc_final: 0.8774 (pt) REVERT: H 815 MET cc_start: 0.8683 (tpt) cc_final: 0.8449 (tpp) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1635 time to fit residues: 99.1674 Evaluate side-chains 188 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS B 152 ASN B 240 GLN B 291 GLN B 435 ASN B 766 ASN C 449 GLN ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS F 210 HIS G 152 ASN G 282 ASN G 531 GLN G 698 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 ASN H 523 GLN H 620 GLN ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 819 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087951 restraints weight = 48948.956| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.09 r_work: 0.3045 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25892 Z= 0.164 Angle : 0.648 10.466 35112 Z= 0.336 Chirality : 0.046 0.186 3834 Planarity : 0.005 0.060 4494 Dihedral : 6.150 60.768 3426 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.12 % Allowed : 5.29 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.24 (0.15), residues: 3120 helix: 0.84 (0.18), residues: 812 sheet: 0.16 (0.18), residues: 778 loop : -0.09 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 728 TYR 0.024 0.002 TYR A 116 PHE 0.026 0.002 PHE G 756 TRP 0.021 0.002 TRP H 481 HIS 0.010 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00376 (25878) covalent geometry : angle 0.64639 (35106) hydrogen bonds : bond 0.04716 ( 971) hydrogen bonds : angle 5.58251 ( 2754) metal coordination : bond 0.01287 ( 14) metal coordination : angle 3.96602 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8622 (m-80) cc_final: 0.8232 (m-80) REVERT: A 138 MET cc_start: 0.8652 (tmm) cc_final: 0.8222 (ptm) REVERT: A 178 TYR cc_start: 0.8674 (t80) cc_final: 0.8465 (t80) REVERT: B 170 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (t) REVERT: B 174 CYS cc_start: 0.7828 (m) cc_final: 0.7509 (m) REVERT: B 549 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8463 (mmmm) REVERT: B 555 GLN cc_start: 0.8605 (tp40) cc_final: 0.8302 (tp-100) REVERT: B 681 MET cc_start: 0.9312 (tpt) cc_final: 0.8868 (tpp) REVERT: B 685 ARG cc_start: 0.8940 (mmm-85) cc_final: 0.8300 (tpp80) REVERT: B 710 ARG cc_start: 0.9251 (ptt-90) cc_final: 0.8999 (ptt90) REVERT: B 770 TRP cc_start: 0.7623 (m100) cc_final: 0.7332 (m100) REVERT: C 737 MET cc_start: 0.8891 (mmt) cc_final: 0.8557 (mmt) REVERT: F 116 TYR cc_start: 0.8271 (m-80) cc_final: 0.7797 (m-10) REVERT: F 138 MET cc_start: 0.7669 (ptm) cc_final: 0.6892 (ptm) REVERT: F 211 TYR cc_start: 0.8846 (t80) cc_final: 0.8571 (t80) REVERT: G 103 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8515 (p) REVERT: G 681 MET cc_start: 0.9430 (tpp) cc_final: 0.9082 (tpp) REVERT: G 743 PHE cc_start: 0.8308 (m-80) cc_final: 0.8063 (m-80) REVERT: G 805 TRP cc_start: 0.8640 (p-90) cc_final: 0.8360 (p-90) REVERT: H 489 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7656 (pttt) REVERT: H 563 MET cc_start: 0.8813 (ttt) cc_final: 0.8564 (ttt) outliers start: 31 outliers final: 15 residues processed: 239 average time/residue: 0.1717 time to fit residues: 64.8744 Evaluate side-chains 192 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 725 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 243 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 138 optimal weight: 0.0980 chunk 71 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN C 857 GLN F 194 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 HIS H 523 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088855 restraints weight = 49029.189| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.19 r_work: 0.3047 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25892 Z= 0.128 Angle : 0.584 11.278 35112 Z= 0.297 Chirality : 0.044 0.208 3834 Planarity : 0.004 0.055 4494 Dihedral : 5.520 59.852 3426 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.12 % Allowed : 6.55 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.48 (0.15), residues: 3120 helix: 1.32 (0.18), residues: 806 sheet: 0.10 (0.18), residues: 792 loop : 0.01 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 222 TYR 0.016 0.001 TYR A 116 PHE 0.032 0.001 PHE G 756 TRP 0.013 0.001 TRP H 481 HIS 0.011 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00282 (25878) covalent geometry : angle 0.58206 (35106) hydrogen bonds : bond 0.03874 ( 971) hydrogen bonds : angle 5.07276 ( 2754) metal coordination : bond 0.01086 ( 14) metal coordination : angle 3.91869 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7514 (m) REVERT: A 138 MET cc_start: 0.8702 (tmm) cc_final: 0.8299 (ptm) REVERT: A 178 TYR cc_start: 0.8647 (t80) cc_final: 0.8427 (t80) REVERT: B 555 GLN cc_start: 0.8704 (tp40) cc_final: 0.8449 (tp-100) REVERT: B 681 MET cc_start: 0.9408 (tpt) cc_final: 0.9119 (tpp) REVERT: B 685 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.7874 (mmm160) REVERT: B 688 MET cc_start: 0.8694 (mtp) cc_final: 0.8460 (mtp) REVERT: B 710 ARG cc_start: 0.9260 (ptt-90) cc_final: 0.9039 (ptt-90) REVERT: C 387 TRP cc_start: 0.7977 (m-10) cc_final: 0.7714 (m-10) REVERT: C 737 MET cc_start: 0.8869 (mmt) cc_final: 0.8622 (mmt) REVERT: F 138 MET cc_start: 0.7932 (ptm) cc_final: 0.7193 (ptm) REVERT: F 159 TYR cc_start: 0.8787 (t80) cc_final: 0.8499 (t80) REVERT: F 211 TYR cc_start: 0.8870 (t80) cc_final: 0.8661 (t80) REVERT: G 103 VAL cc_start: 0.8772 (m) cc_final: 0.8516 (p) REVERT: G 681 MET cc_start: 0.9428 (tpp) cc_final: 0.9114 (tpp) REVERT: G 696 TYR cc_start: 0.9131 (t80) cc_final: 0.8565 (t80) REVERT: G 743 PHE cc_start: 0.8331 (m-80) cc_final: 0.8110 (m-80) REVERT: G 805 TRP cc_start: 0.8714 (p-90) cc_final: 0.8420 (p-90) REVERT: H 489 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7586 (pttt) REVERT: H 563 MET cc_start: 0.8808 (ttt) cc_final: 0.8575 (ttt) REVERT: H 888 MET cc_start: 0.8572 (ttm) cc_final: 0.8112 (ttm) outliers start: 31 outliers final: 18 residues processed: 217 average time/residue: 0.1752 time to fit residues: 61.3976 Evaluate side-chains 188 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 847 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 847 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 308 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 0.0470 chunk 132 optimal weight: 0.0270 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN C 312 HIS C 570 HIS C 674 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.122994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088114 restraints weight = 48680.467| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.14 r_work: 0.3049 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25892 Z= 0.128 Angle : 0.556 9.986 35112 Z= 0.281 Chirality : 0.043 0.185 3834 Planarity : 0.004 0.054 4494 Dihedral : 5.208 60.177 3426 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.41 % Allowed : 7.42 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.52 (0.15), residues: 3120 helix: 1.50 (0.19), residues: 818 sheet: 0.06 (0.18), residues: 802 loop : -0.03 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 195 TYR 0.030 0.001 TYR A 116 PHE 0.017 0.001 PHE B 239 TRP 0.023 0.001 TRP B 770 HIS 0.008 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00298 (25878) covalent geometry : angle 0.55585 (35106) hydrogen bonds : bond 0.03537 ( 971) hydrogen bonds : angle 4.86020 ( 2754) metal coordination : bond 0.00464 ( 14) metal coordination : angle 1.66378 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 CYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7469 (m) REVERT: A 138 MET cc_start: 0.8728 (tmm) cc_final: 0.8326 (ptm) REVERT: A 178 TYR cc_start: 0.8630 (t80) cc_final: 0.8369 (t80) REVERT: B 555 GLN cc_start: 0.8667 (tp40) cc_final: 0.8385 (tp-100) REVERT: B 681 MET cc_start: 0.9432 (tpt) cc_final: 0.8813 (tpp) REVERT: B 685 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8452 (ttm110) REVERT: B 710 ARG cc_start: 0.9316 (ptt-90) cc_final: 0.9106 (ptt90) REVERT: C 387 TRP cc_start: 0.7996 (m-10) cc_final: 0.7577 (m-10) REVERT: C 737 MET cc_start: 0.8861 (mmt) cc_final: 0.8475 (mmt) REVERT: F 116 TYR cc_start: 0.8017 (m-80) cc_final: 0.7758 (m-10) REVERT: F 138 MET cc_start: 0.7824 (ptm) cc_final: 0.7093 (ptm) REVERT: F 159 TYR cc_start: 0.8759 (t80) cc_final: 0.8543 (t80) REVERT: G 665 MET cc_start: 0.8503 (ttt) cc_final: 0.7873 (tmm) REVERT: G 681 MET cc_start: 0.9417 (tpp) cc_final: 0.9109 (tpp) REVERT: G 743 PHE cc_start: 0.8369 (m-80) cc_final: 0.8160 (m-80) REVERT: G 805 TRP cc_start: 0.8739 (p-90) cc_final: 0.8462 (p-90) REVERT: H 489 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7515 (pttt) REVERT: H 888 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8096 (ttm) outliers start: 39 outliers final: 17 residues processed: 213 average time/residue: 0.1579 time to fit residues: 54.3130 Evaluate side-chains 189 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 292 optimal weight: 0.0370 chunk 229 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 293 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 HIS C 523 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS F 248 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 704 ASN ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 857 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.122966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087831 restraints weight = 48771.867| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.02 r_work: 0.3043 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25892 Z= 0.131 Angle : 0.549 10.335 35112 Z= 0.276 Chirality : 0.044 0.318 3834 Planarity : 0.004 0.049 4494 Dihedral : 5.032 60.136 3426 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 7.78 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.57 (0.15), residues: 3120 helix: 1.67 (0.19), residues: 818 sheet: 0.04 (0.18), residues: 800 loop : -0.05 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 566 TYR 0.015 0.001 TYR G 353 PHE 0.017 0.001 PHE B 239 TRP 0.016 0.001 TRP C 337 HIS 0.007 0.001 HIS G 733 Details of bonding type rmsd covalent geometry : bond 0.00306 (25878) covalent geometry : angle 0.54823 (35106) hydrogen bonds : bond 0.03394 ( 971) hydrogen bonds : angle 4.75656 ( 2754) metal coordination : bond 0.00409 ( 14) metal coordination : angle 1.99459 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8775 (ptp) cc_final: 0.8462 (ppp) REVERT: A 136 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7706 (m) REVERT: A 138 MET cc_start: 0.8696 (tmm) cc_final: 0.8349 (ptm) REVERT: A 178 TYR cc_start: 0.8656 (t80) cc_final: 0.8383 (t80) REVERT: B 555 GLN cc_start: 0.8654 (tp40) cc_final: 0.8337 (tp-100) REVERT: B 681 MET cc_start: 0.9433 (tpt) cc_final: 0.9141 (tpp) REVERT: B 685 ARG cc_start: 0.8868 (mmm-85) cc_final: 0.8130 (ttm-80) REVERT: C 319 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7850 (mt-10) REVERT: C 387 TRP cc_start: 0.8025 (m-10) cc_final: 0.7631 (m-10) REVERT: C 677 CYS cc_start: 0.8812 (p) cc_final: 0.8604 (p) REVERT: C 737 MET cc_start: 0.8836 (mmt) cc_final: 0.8533 (mmt) REVERT: F 116 TYR cc_start: 0.8104 (m-80) cc_final: 0.7831 (m-10) REVERT: F 138 MET cc_start: 0.7943 (ptm) cc_final: 0.7213 (ptm) REVERT: G 103 VAL cc_start: 0.8732 (m) cc_final: 0.8482 (p) REVERT: G 665 MET cc_start: 0.8435 (ttt) cc_final: 0.7914 (tmm) REVERT: G 681 MET cc_start: 0.9402 (tpp) cc_final: 0.9095 (tpp) REVERT: G 688 MET cc_start: 0.9208 (mmm) cc_final: 0.8886 (mmt) REVERT: G 696 TYR cc_start: 0.9005 (t80) cc_final: 0.8413 (t80) REVERT: G 743 PHE cc_start: 0.8335 (m-80) cc_final: 0.7952 (m-80) REVERT: G 805 TRP cc_start: 0.8743 (p-90) cc_final: 0.8454 (p-90) REVERT: H 489 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7545 (pttt) REVERT: H 888 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8150 (ttm) outliers start: 43 outliers final: 23 residues processed: 213 average time/residue: 0.1553 time to fit residues: 53.4030 Evaluate side-chains 191 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 199 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 178 optimal weight: 0.0040 chunk 90 optimal weight: 10.0000 chunk 222 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 620 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS F 248 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088436 restraints weight = 48610.221| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.10 r_work: 0.3067 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25892 Z= 0.106 Angle : 0.532 11.456 35112 Z= 0.267 Chirality : 0.043 0.283 3834 Planarity : 0.004 0.046 4494 Dihedral : 4.845 59.600 3426 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.27 % Allowed : 8.65 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.67 (0.15), residues: 3120 helix: 1.74 (0.19), residues: 818 sheet: 0.11 (0.18), residues: 812 loop : 0.00 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 195 TYR 0.013 0.001 TYR A 373 PHE 0.014 0.001 PHE G 756 TRP 0.015 0.001 TRP B 805 HIS 0.006 0.001 HIS G 733 Details of bonding type rmsd covalent geometry : bond 0.00239 (25878) covalent geometry : angle 0.53117 (35106) hydrogen bonds : bond 0.03231 ( 971) hydrogen bonds : angle 4.62483 ( 2754) metal coordination : bond 0.00450 ( 14) metal coordination : angle 1.96410 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8769 (ptp) cc_final: 0.8492 (ppp) REVERT: A 136 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7674 (m) REVERT: A 138 MET cc_start: 0.8675 (tmm) cc_final: 0.8363 (ptm) REVERT: A 178 TYR cc_start: 0.8681 (t80) cc_final: 0.8406 (t80) REVERT: A 373 TYR cc_start: 0.9066 (t80) cc_final: 0.8825 (t80) REVERT: B 332 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 555 GLN cc_start: 0.8575 (tp40) cc_final: 0.8304 (tp-100) REVERT: B 681 MET cc_start: 0.9385 (tpt) cc_final: 0.9056 (tpp) REVERT: B 685 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8090 (ttm-80) REVERT: C 319 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 387 TRP cc_start: 0.7978 (m-10) cc_final: 0.7562 (m-10) REVERT: C 737 MET cc_start: 0.8827 (mmt) cc_final: 0.8560 (mmt) REVERT: F 116 TYR cc_start: 0.8033 (m-80) cc_final: 0.7776 (m-10) REVERT: F 138 MET cc_start: 0.8050 (ptm) cc_final: 0.7332 (ptm) REVERT: G 103 VAL cc_start: 0.8704 (m) cc_final: 0.8459 (p) REVERT: G 665 MET cc_start: 0.8359 (ttt) cc_final: 0.7828 (tmm) REVERT: G 681 MET cc_start: 0.9353 (tpp) cc_final: 0.9050 (tpp) REVERT: G 688 MET cc_start: 0.9169 (mmm) cc_final: 0.8609 (mmt) REVERT: G 696 TYR cc_start: 0.9020 (t80) cc_final: 0.8437 (t80) REVERT: G 738 MET cc_start: 0.6737 (ppp) cc_final: 0.6320 (ppp) REVERT: G 805 TRP cc_start: 0.8735 (p-90) cc_final: 0.8457 (p-90) REVERT: H 888 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8058 (ttm) outliers start: 35 outliers final: 22 residues processed: 204 average time/residue: 0.1631 time to fit residues: 53.5717 Evaluate side-chains 190 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 588 MET Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 144 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 181 optimal weight: 0.3980 chunk 250 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088590 restraints weight = 48895.261| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.20 r_work: 0.3046 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25892 Z= 0.117 Angle : 0.531 11.621 35112 Z= 0.266 Chirality : 0.043 0.302 3834 Planarity : 0.004 0.044 4494 Dihedral : 4.760 58.482 3426 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.41 % Allowed : 8.94 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.66 (0.15), residues: 3120 helix: 1.81 (0.19), residues: 818 sheet: 0.06 (0.18), residues: 800 loop : -0.02 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 710 TYR 0.015 0.001 TYR G 353 PHE 0.016 0.001 PHE G 756 TRP 0.013 0.001 TRP B 805 HIS 0.006 0.001 HIS G 733 Details of bonding type rmsd covalent geometry : bond 0.00271 (25878) covalent geometry : angle 0.53037 (35106) hydrogen bonds : bond 0.03194 ( 971) hydrogen bonds : angle 4.57038 ( 2754) metal coordination : bond 0.00429 ( 14) metal coordination : angle 1.99361 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8802 (ptp) cc_final: 0.8507 (ppp) REVERT: A 136 CYS cc_start: 0.8642 (m) cc_final: 0.7699 (m) REVERT: A 138 MET cc_start: 0.8713 (tmm) cc_final: 0.8351 (ptm) REVERT: A 178 TYR cc_start: 0.8624 (t80) cc_final: 0.8394 (t80) REVERT: A 373 TYR cc_start: 0.9099 (t80) cc_final: 0.8845 (t80) REVERT: B 332 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 555 GLN cc_start: 0.8621 (tp40) cc_final: 0.8323 (tp-100) REVERT: B 681 MET cc_start: 0.9448 (tpt) cc_final: 0.9105 (tpp) REVERT: B 685 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8131 (ttm-80) REVERT: C 319 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7873 (mt-10) REVERT: C 387 TRP cc_start: 0.7956 (m-10) cc_final: 0.7541 (m-10) REVERT: C 737 MET cc_start: 0.8801 (mmt) cc_final: 0.8526 (mmt) REVERT: F 116 TYR cc_start: 0.8143 (m-80) cc_final: 0.7866 (m-10) REVERT: F 138 MET cc_start: 0.8050 (ptm) cc_final: 0.7337 (ptm) REVERT: G 89 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8707 (mt) REVERT: G 103 VAL cc_start: 0.8755 (m) cc_final: 0.8471 (p) REVERT: G 665 MET cc_start: 0.8379 (ttt) cc_final: 0.7893 (tmm) REVERT: G 681 MET cc_start: 0.9397 (tpp) cc_final: 0.9107 (tpp) REVERT: G 688 MET cc_start: 0.9132 (mmm) cc_final: 0.8783 (mmt) REVERT: G 696 TYR cc_start: 0.9063 (t80) cc_final: 0.8432 (t80) REVERT: G 805 TRP cc_start: 0.8756 (p-90) cc_final: 0.8410 (p-90) REVERT: H 523 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7476 (tp-100) REVERT: H 888 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8132 (ttm) outliers start: 39 outliers final: 24 residues processed: 206 average time/residue: 0.1683 time to fit residues: 55.6210 Evaluate side-chains 197 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 588 MET Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 810 LEU Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 70 optimal weight: 4.9990 chunk 222 optimal weight: 0.0980 chunk 237 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 186 optimal weight: 0.0970 chunk 257 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS F 248 HIS G 289 GLN ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.124152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089670 restraints weight = 48864.578| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.28 r_work: 0.3073 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25892 Z= 0.097 Angle : 0.532 17.701 35112 Z= 0.265 Chirality : 0.042 0.276 3834 Planarity : 0.004 0.045 4494 Dihedral : 4.598 56.745 3426 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.23 % Allowed : 9.38 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.76 (0.15), residues: 3120 helix: 1.88 (0.19), residues: 820 sheet: 0.12 (0.18), residues: 824 loop : 0.06 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 710 TYR 0.012 0.001 TYR B 777 PHE 0.031 0.001 PHE G 743 TRP 0.021 0.001 TRP G 805 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00215 (25878) covalent geometry : angle 0.53140 (35106) hydrogen bonds : bond 0.03033 ( 971) hydrogen bonds : angle 4.48140 ( 2754) metal coordination : bond 0.00562 ( 14) metal coordination : angle 2.04586 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8781 (ptp) cc_final: 0.8513 (ppp) REVERT: A 136 CYS cc_start: 0.8592 (m) cc_final: 0.7738 (m) REVERT: A 138 MET cc_start: 0.8735 (tmm) cc_final: 0.8375 (ptm) REVERT: A 373 TYR cc_start: 0.9109 (t80) cc_final: 0.8867 (t80) REVERT: A 402 MET cc_start: 0.8498 (mmm) cc_final: 0.7958 (tpt) REVERT: B 328 MET cc_start: 0.8575 (tpp) cc_final: 0.8025 (mmm) REVERT: B 332 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 681 MET cc_start: 0.9424 (tpt) cc_final: 0.9084 (tpp) REVERT: B 685 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8123 (ttm-80) REVERT: C 319 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7661 (mt-10) REVERT: C 387 TRP cc_start: 0.7914 (m-10) cc_final: 0.7595 (m-10) REVERT: C 737 MET cc_start: 0.8812 (mmt) cc_final: 0.8552 (mmt) REVERT: F 116 TYR cc_start: 0.8143 (m-80) cc_final: 0.7900 (m-10) REVERT: F 138 MET cc_start: 0.8062 (ptm) cc_final: 0.7355 (ptm) REVERT: G 89 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8677 (mt) REVERT: G 103 VAL cc_start: 0.8750 (m) cc_final: 0.8462 (p) REVERT: G 665 MET cc_start: 0.8348 (ttt) cc_final: 0.7937 (tmm) REVERT: G 681 MET cc_start: 0.9375 (tpp) cc_final: 0.9098 (tpp) REVERT: G 688 MET cc_start: 0.9101 (mmm) cc_final: 0.8807 (mmt) REVERT: G 696 TYR cc_start: 0.9093 (t80) cc_final: 0.8521 (t80) REVERT: G 754 LEU cc_start: 0.7423 (mm) cc_final: 0.6721 (mm) REVERT: G 805 TRP cc_start: 0.8484 (p-90) cc_final: 0.8216 (p-90) REVERT: H 478 SER cc_start: 0.9122 (p) cc_final: 0.8720 (m) REVERT: H 523 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7471 (tp-100) REVERT: H 815 MET cc_start: 0.8081 (mmm) cc_final: 0.7749 (tmm) REVERT: H 888 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8126 (ttm) outliers start: 34 outliers final: 22 residues processed: 215 average time/residue: 0.1690 time to fit residues: 57.8218 Evaluate side-chains 199 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 588 MET Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 648 GLU Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 51 optimal weight: 2.9990 chunk 228 optimal weight: 0.0040 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 260 optimal weight: 0.0050 chunk 86 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 GLN B 478 HIS C 322 HIS C 592 GLN ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 HIS ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086543 restraints weight = 48973.759| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.09 r_work: 0.3018 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25892 Z= 0.182 Angle : 0.581 14.849 35112 Z= 0.289 Chirality : 0.044 0.277 3834 Planarity : 0.004 0.045 4494 Dihedral : 4.755 54.812 3426 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.38 % Allowed : 9.81 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.59 (0.15), residues: 3120 helix: 1.88 (0.19), residues: 818 sheet: -0.10 (0.18), residues: 812 loop : -0.07 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 710 TYR 0.021 0.001 TYR C 755 PHE 0.036 0.002 PHE G 743 TRP 0.016 0.001 TRP H 481 HIS 0.006 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00437 (25878) covalent geometry : angle 0.57990 (35106) hydrogen bonds : bond 0.03365 ( 971) hydrogen bonds : angle 4.62863 ( 2754) metal coordination : bond 0.00410 ( 14) metal coordination : angle 2.12006 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8793 (ptp) cc_final: 0.8527 (ppp) REVERT: A 136 CYS cc_start: 0.8596 (m) cc_final: 0.7786 (m) REVERT: A 138 MET cc_start: 0.8766 (tmm) cc_final: 0.8414 (ptm) REVERT: A 373 TYR cc_start: 0.9116 (t80) cc_final: 0.8863 (t80) REVERT: A 402 MET cc_start: 0.8534 (mmm) cc_final: 0.8007 (tpt) REVERT: B 328 MET cc_start: 0.8558 (tpp) cc_final: 0.8020 (mmm) REVERT: B 332 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8078 (mt) REVERT: B 681 MET cc_start: 0.9414 (tpt) cc_final: 0.8947 (tpp) REVERT: B 685 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8450 (ttm110) REVERT: C 319 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7880 (mt-10) REVERT: C 387 TRP cc_start: 0.8028 (m-10) cc_final: 0.7737 (m-10) REVERT: C 737 MET cc_start: 0.8788 (mmt) cc_final: 0.8486 (mmt) REVERT: F 116 TYR cc_start: 0.8197 (m-80) cc_final: 0.7965 (m-10) REVERT: F 138 MET cc_start: 0.8011 (ptm) cc_final: 0.7796 (ptm) REVERT: G 665 MET cc_start: 0.8315 (ttt) cc_final: 0.7885 (tmm) REVERT: G 681 MET cc_start: 0.9378 (tpp) cc_final: 0.9144 (tpp) REVERT: G 696 TYR cc_start: 0.9093 (t80) cc_final: 0.8561 (t80) REVERT: G 754 LEU cc_start: 0.7481 (mm) cc_final: 0.6885 (mm) REVERT: G 805 TRP cc_start: 0.8582 (p-90) cc_final: 0.8292 (p-90) REVERT: H 523 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7474 (tp-100) REVERT: H 888 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8123 (ttm) outliers start: 38 outliers final: 24 residues processed: 211 average time/residue: 0.1703 time to fit residues: 57.9859 Evaluate side-chains 202 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 588 MET Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 0.5980 chunk 253 optimal weight: 0.0270 chunk 114 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.122937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088010 restraints weight = 48886.301| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.09 r_work: 0.3046 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25892 Z= 0.117 Angle : 0.557 15.126 35112 Z= 0.277 Chirality : 0.043 0.335 3834 Planarity : 0.004 0.045 4494 Dihedral : 4.658 54.233 3426 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.05 % Allowed : 10.21 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.59 (0.15), residues: 3120 helix: 1.82 (0.19), residues: 820 sheet: -0.10 (0.18), residues: 812 loop : -0.03 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 710 TYR 0.019 0.001 TYR G 353 PHE 0.038 0.001 PHE G 743 TRP 0.017 0.001 TRP G 805 HIS 0.009 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00272 (25878) covalent geometry : angle 0.55625 (35106) hydrogen bonds : bond 0.03195 ( 971) hydrogen bonds : angle 4.58738 ( 2754) metal coordination : bond 0.00475 ( 14) metal coordination : angle 2.07703 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8272 (tmm) cc_final: 0.7796 (tmm) REVERT: A 102 MET cc_start: 0.8805 (ptp) cc_final: 0.8530 (ppp) REVERT: A 136 CYS cc_start: 0.8611 (m) cc_final: 0.7800 (m) REVERT: A 138 MET cc_start: 0.8750 (tmm) cc_final: 0.8395 (ptm) REVERT: A 373 TYR cc_start: 0.9101 (t80) cc_final: 0.8861 (t80) REVERT: A 402 MET cc_start: 0.8484 (mmm) cc_final: 0.7980 (tpt) REVERT: B 328 MET cc_start: 0.8516 (tpp) cc_final: 0.7958 (mmm) REVERT: B 332 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8087 (mt) REVERT: B 681 MET cc_start: 0.9437 (tpt) cc_final: 0.9045 (tpp) REVERT: B 685 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.7831 (mtp85) REVERT: B 688 MET cc_start: 0.8604 (mtp) cc_final: 0.8389 (mtm) REVERT: C 319 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 387 TRP cc_start: 0.7984 (m-10) cc_final: 0.7744 (m-10) REVERT: C 737 MET cc_start: 0.8786 (mmt) cc_final: 0.8514 (mmt) REVERT: F 116 TYR cc_start: 0.8244 (m-80) cc_final: 0.8014 (m-10) REVERT: F 138 MET cc_start: 0.8082 (ptm) cc_final: 0.7399 (ptm) REVERT: G 103 VAL cc_start: 0.8696 (m) cc_final: 0.8468 (p) REVERT: G 665 MET cc_start: 0.8344 (ttt) cc_final: 0.7927 (tmm) REVERT: G 681 MET cc_start: 0.9371 (tpp) cc_final: 0.9100 (tpp) REVERT: G 696 TYR cc_start: 0.9122 (t80) cc_final: 0.8592 (t80) REVERT: G 754 LEU cc_start: 0.7405 (mm) cc_final: 0.6793 (mm) REVERT: G 805 TRP cc_start: 0.8557 (p-90) cc_final: 0.8240 (p-90) REVERT: H 523 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7492 (tp-100) REVERT: H 888 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8124 (ttm) outliers start: 29 outliers final: 22 residues processed: 200 average time/residue: 0.1508 time to fit residues: 49.2894 Evaluate side-chains 198 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 824 HIS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 588 MET Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain G residue 771 LEU Chi-restraints excluded: chain G residue 814 CYS Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 523 GLN Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain H residue 810 LEU Chi-restraints excluded: chain H residue 811 ARG Chi-restraints excluded: chain H residue 847 ASP Chi-restraints excluded: chain H residue 866 VAL Chi-restraints excluded: chain H residue 888 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 138 optimal weight: 0.0870 chunk 204 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 290 optimal weight: 0.8980 chunk 72 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 HIS ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088748 restraints weight = 48710.373| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.10 r_work: 0.3050 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25892 Z= 0.112 Angle : 0.558 14.762 35112 Z= 0.276 Chirality : 0.043 0.344 3834 Planarity : 0.004 0.045 4494 Dihedral : 4.590 52.914 3426 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.12 % Allowed : 10.35 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 aren not related in a simple way. whole: 0.61 (0.15), residues: 3120 helix: 1.84 (0.19), residues: 820 sheet: -0.10 (0.18), residues: 812 loop : -0.01 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 710 TYR 0.026 0.001 TYR B 785 PHE 0.039 0.001 PHE G 743 TRP 0.016 0.001 TRP G 805 HIS 0.007 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00256 (25878) covalent geometry : angle 0.55684 (35106) hydrogen bonds : bond 0.03134 ( 971) hydrogen bonds : angle 4.54768 ( 2754) metal coordination : bond 0.00503 ( 14) metal coordination : angle 2.16621 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6105.00 seconds wall clock time: 105 minutes 40.22 seconds (6340.22 seconds total)