Starting phenix.real_space_refine on Mon Aug 25 19:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxh_29533/08_2025/8fxh_29533.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 19284 2.51 5 N 5070 2.21 5 O 5790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s 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: 30228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "B" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "C" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "D" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "E" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain: "F" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5038 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Time building chain proxies: 8.48, per 1000 atoms: 0.28 Number of scatterers: 30228 At special positions: 0 Unit cell: (152.55, 188.325, 162.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 5790 8.00 N 5070 7.00 C 19284 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 34 sheets defined 35.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 removed outlier: 4.090A pdb=" N TYR A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.669A pdb=" N TYR A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.742A pdb=" N LEU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.716A pdb=" N SER A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.590A pdb=" N HIS A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 removed outlier: 4.186A pdb=" N VAL A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 470 through 479 removed outlier: 4.020A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.620A pdb=" N ALA A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'A' and resid 496 through 509 Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.946A pdb=" N ASN A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.644A pdb=" N LEU A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 589 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.692A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.848A pdb=" N TYR B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.782A pdb=" N LEU B 69 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 70' Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.646A pdb=" N LEU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.548A pdb=" N ASN B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.860A pdb=" N ALA B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.709A pdb=" N SER B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.820A pdb=" N LEU B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.604A pdb=" N LYS B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.652A pdb=" N SER B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 408 through 420 Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.181A pdb=" N ARG B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.936A pdb=" N ARG B 486 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.590A pdb=" N MET B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.561A pdb=" N ASN B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 624 through 629 removed outlier: 3.602A pdb=" N TYR B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 624 through 629' Processing helix chain 'C' and resid 54 through 64 removed outlier: 4.207A pdb=" N TYR C 58 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.989A pdb=" N LYS C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.579A pdb=" N LEU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 137 removed outlier: 3.725A pdb=" N GLN C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.857A pdb=" N ALA C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.729A pdb=" N GLN C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.790A pdb=" N SER C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.687A pdb=" N VAL C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.609A pdb=" N ALA C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.546A pdb=" N SER C 345 " --> pdb=" O LYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.786A pdb=" N HIS C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 407 removed outlier: 4.256A pdb=" N VAL C 407 " --> pdb=" O THR C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 407' Processing helix chain 'C' and resid 408 through 420 Processing helix chain 'C' and resid 469 through 477 removed outlier: 4.151A pdb=" N ARG C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.964A pdb=" N ARG C 486 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 509 removed outlier: 3.594A pdb=" N LEU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 547 removed outlier: 4.080A pdb=" N ASN C 540 " --> pdb=" O HIS C 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 541 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 542 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 565 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 624 through 629 Processing helix chain 'D' and resid 54 through 64 removed outlier: 4.207A pdb=" N TYR D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 removed outlier: 3.988A pdb=" N LYS D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.578A pdb=" N LEU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.725A pdb=" N GLN D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 161 through 174 removed outlier: 3.857A pdb=" N ALA D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.731A pdb=" N GLN D 195 " --> pdb=" O GLY D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.789A pdb=" N SER D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.686A pdb=" N VAL D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.609A pdb=" N ALA D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.547A pdb=" N SER D 345 " --> pdb=" O LYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 removed outlier: 3.786A pdb=" N HIS D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 407 removed outlier: 4.256A pdb=" N VAL D 407 " --> pdb=" O THR D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 407' Processing helix chain 'D' and resid 408 through 420 Processing helix chain 'D' and resid 469 through 477 removed outlier: 4.151A pdb=" N ARG D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 477 " --> pdb=" O ARG D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 486 removed outlier: 3.964A pdb=" N ARG D 486 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 509 removed outlier: 3.594A pdb=" N LEU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 removed outlier: 4.080A pdb=" N ASN D 540 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 541 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.848A pdb=" N TYR E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.781A pdb=" N LEU E 69 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 70' Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.647A pdb=" N LEU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 136 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.548A pdb=" N ASN E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 removed outlier: 3.860A pdb=" N ALA E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.708A pdb=" N SER E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 227 removed outlier: 3.820A pdb=" N LEU E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 250 removed outlier: 3.604A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E 249 " --> pdb=" O GLU E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 334 through 345 removed outlier: 3.652A pdb=" N SER E 345 " --> pdb=" O LYS E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 408 through 420 Processing helix chain 'E' and resid 469 through 479 removed outlier: 4.181A pdb=" N ARG E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE E 478 " --> pdb=" O ILE E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 486 removed outlier: 3.936A pdb=" N ARG E 486 " --> pdb=" O LYS E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 509 removed outlier: 3.591A pdb=" N MET E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 547 removed outlier: 3.561A pdb=" N ASN E 547 " --> pdb=" O ASN E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 583 through 589 Processing helix chain 'E' and resid 624 through 629 removed outlier: 3.601A pdb=" N TYR E 628 " --> pdb=" O ILE E 624 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 629 " --> pdb=" O GLU E 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 624 through 629' Processing helix chain 'F' and resid 54 through 61 removed outlier: 4.089A pdb=" N TYR F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.670A pdb=" N TYR F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 89 removed outlier: 3.742A pdb=" N LEU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 134 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 161 through 174 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.717A pdb=" N SER F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 336 through 344 Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.590A pdb=" N HIS F 366 " --> pdb=" O ASP F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 407 removed outlier: 4.186A pdb=" N VAL F 407 " --> pdb=" O THR F 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 407' Processing helix chain 'F' and resid 408 through 420 Processing helix chain 'F' and resid 470 through 479 removed outlier: 4.020A pdb=" N PHE F 478 " --> pdb=" O ILE F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 486 removed outlier: 3.621A pdb=" N ALA F 485 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 486 " --> pdb=" O LYS F 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 482 through 486' Processing helix chain 'F' and resid 496 through 509 Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.946A pdb=" N ASN F 540 " --> pdb=" O HIS F 536 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 541 " --> pdb=" O TYR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 583 through 589 removed outlier: 3.643A pdb=" N LEU F 587 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 589 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 632 removed outlier: 3.692A pdb=" N VAL F 627 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS F 630 " --> pdb=" O GLN F 626 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 631 " --> pdb=" O VAL F 627 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 5.980A pdb=" N ASN A 24 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A 43 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.841A pdb=" N LEU A 310 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 319 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG A 308 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU A 321 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP A 306 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 449 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 432 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE A 447 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 530 removed outlier: 6.295A pdb=" N ILE A 490 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 597 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 28 removed outlier: 5.420A pdb=" N ILE B 22 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 45 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN B 24 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP B 43 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 109 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 105 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.584A pdb=" N LEU B 186 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.511A pdb=" N ASP B 270 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 254 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.388A pdb=" N PHE B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 312 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 318 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 310 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP B 306 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 449 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 432 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 447 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 526 removed outlier: 3.621A pdb=" N GLU B 556 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE B 490 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 574 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 21 through 28 removed outlier: 4.268A pdb=" N VAL C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 41 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN C 27 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA C 39 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 178 through 180 Processing sheet with id=AB5, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB6, first strand: chain 'C' and resid 399 through 402 removed outlier: 6.908A pdb=" N LEU C 310 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA C 319 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG C 308 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU C 321 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP C 306 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 449 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 432 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 447 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 326 through 327 Processing sheet with id=AB8, first strand: chain 'C' and resid 529 through 530 removed outlier: 3.707A pdb=" N GLU C 556 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE C 490 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 574 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 28 removed outlier: 4.268A pdb=" N VAL D 25 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 41 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN D 27 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 39 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 178 through 180 Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'D' and resid 399 through 402 removed outlier: 6.909A pdb=" N LEU D 310 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA D 319 " --> pdb=" O ARG D 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG D 308 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU D 321 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP D 306 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 449 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE D 432 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE D 447 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 326 through 327 Processing sheet with id=AC5, first strand: chain 'D' and resid 529 through 530 removed outlier: 3.706A pdb=" N GLU D 556 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 490 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 574 " --> pdb=" O ILE D 489 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 20 through 28 removed outlier: 5.420A pdb=" N ILE E 22 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA E 45 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN E 24 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP E 43 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN E 109 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 105 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.585A pdb=" N LEU E 186 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 269 through 270 removed outlier: 3.511A pdb=" N ASP E 270 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 254 " --> pdb=" O ASP E 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 399 through 402 removed outlier: 5.389A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 312 " --> pdb=" O PHE E 316 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA E 318 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 310 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 306 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 449 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE E 432 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE E 447 " --> pdb=" O ILE E 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AD2, first strand: chain 'E' and resid 524 through 526 removed outlier: 3.621A pdb=" N GLU E 556 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE E 490 " --> pdb=" O ALA E 555 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 574 " --> pdb=" O ILE E 489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 23 through 28 removed outlier: 5.980A pdb=" N ASN F 24 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP F 43 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 179 through 181 Processing sheet with id=AD5, first strand: chain 'F' and resid 399 through 402 removed outlier: 3.840A pdb=" N LEU F 310 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA F 319 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG F 308 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU F 321 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP F 306 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 449 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 432 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE F 447 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 326 through 327 Processing sheet with id=AD7, first strand: chain 'F' and resid 529 through 530 removed outlier: 6.295A pdb=" N ILE F 490 " --> pdb=" O ALA F 555 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL F 597 " --> pdb=" O LYS F 608 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3084 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: 6.59 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5353 1.32 - 1.44: 7776 1.44 - 1.56: 17571 1.56 - 1.69: 8 1.69 - 1.81: 132 Bond restraints: 30840 Sorted by residual: bond pdb=" C PHE A 132 " pdb=" N GLU A 133 " ideal model delta sigma weight residual 1.335 1.205 0.130 1.31e-02 5.83e+03 9.80e+01 bond pdb=" C PHE F 132 " pdb=" N GLU F 133 " ideal model delta sigma weight residual 1.335 1.206 0.129 1.31e-02 5.83e+03 9.74e+01 bond pdb=" C ILE A 335 " pdb=" N ALA A 336 " ideal model delta sigma weight residual 1.332 1.198 0.135 1.40e-02 5.10e+03 9.26e+01 bond pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 1.473 1.608 -0.135 1.40e-02 5.10e+03 9.23e+01 bond pdb=" N PRO F 253 " pdb=" CD PRO F 253 " ideal model delta sigma weight residual 1.473 1.607 -0.134 1.40e-02 5.10e+03 9.22e+01 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.05: 41792 13.05 - 26.10: 66 26.10 - 39.15: 6 39.15 - 52.20: 2 52.20 - 65.25: 2 Bond angle restraints: 41868 Sorted by residual: angle pdb=" N GLY A 264 " pdb=" CA GLY A 264 " pdb=" C GLY A 264 " ideal model delta sigma weight residual 111.14 176.39 -65.25 1.46e+00 4.69e-01 2.00e+03 angle pdb=" N GLY F 264 " pdb=" CA GLY F 264 " pdb=" C GLY F 264 " ideal model delta sigma weight residual 111.14 176.29 -65.15 1.46e+00 4.69e-01 1.99e+03 angle pdb=" N VAL A 298 " pdb=" CA VAL A 298 " pdb=" C VAL A 298 " ideal model delta sigma weight residual 111.09 152.23 -41.14 1.25e+00 6.40e-01 1.08e+03 angle pdb=" N VAL F 298 " pdb=" CA VAL F 298 " pdb=" C VAL F 298 " ideal model delta sigma weight residual 111.09 152.23 -41.14 1.25e+00 6.40e-01 1.08e+03 angle pdb=" C LYS E 263 " pdb=" CA LYS E 263 " pdb=" CB LYS E 263 " ideal model delta sigma weight residual 116.63 147.89 -31.26 1.16e+00 7.43e-01 7.26e+02 ... (remaining 41863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 16029 17.60 - 35.20: 1779 35.20 - 52.79: 564 52.79 - 70.39: 140 70.39 - 87.99: 52 Dihedral angle restraints: 18564 sinusoidal: 7500 harmonic: 11064 Sorted by residual: dihedral pdb=" C HIS A 262 " pdb=" N HIS A 262 " pdb=" CA HIS A 262 " pdb=" CB HIS A 262 " ideal model delta harmonic sigma weight residual -122.60 -178.51 55.91 0 2.50e+00 1.60e-01 5.00e+02 dihedral pdb=" C HIS F 262 " pdb=" N HIS F 262 " pdb=" CA HIS F 262 " pdb=" CB HIS F 262 " ideal model delta harmonic sigma weight residual -122.60 -178.49 55.89 0 2.50e+00 1.60e-01 5.00e+02 dihedral pdb=" N HIS A 262 " pdb=" C HIS A 262 " pdb=" CA HIS A 262 " pdb=" CB HIS A 262 " ideal model delta harmonic sigma weight residual 122.80 177.97 -55.17 0 2.50e+00 1.60e-01 4.87e+02 ... (remaining 18561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.488: 4714 0.488 - 0.976: 18 0.976 - 1.464: 4 1.464 - 1.952: 2 1.952 - 2.440: 2 Chirality restraints: 4740 Sorted by residual: chirality pdb=" CA HIS A 262 " pdb=" N HIS A 262 " pdb=" C HIS A 262 " pdb=" CB HIS A 262 " both_signs ideal model delta sigma weight residual False 2.51 0.07 2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" CA HIS F 262 " pdb=" N HIS F 262 " pdb=" C HIS F 262 " pdb=" CB HIS F 262 " both_signs ideal model delta sigma weight residual False 2.51 0.07 2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" CA VAL A 298 " pdb=" N VAL A 298 " pdb=" C VAL A 298 " pdb=" CB VAL A 298 " both_signs ideal model delta sigma weight residual False 2.44 0.93 1.51 2.00e-01 2.50e+01 5.72e+01 ... (remaining 4737 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 252 " 0.137 5.00e-02 4.00e+02 1.93e-01 5.96e+01 pdb=" N PRO F 253 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO F 253 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO F 253 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " -0.137 5.00e-02 4.00e+02 1.93e-01 5.95e+01 pdb=" N PRO A 253 " 0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 264 " -0.033 2.00e-02 2.50e+03 6.67e-02 4.45e+01 pdb=" C GLY F 264 " 0.115 2.00e-02 2.50e+03 pdb=" O GLY F 264 " -0.042 2.00e-02 2.50e+03 pdb=" N ILE F 265 " -0.040 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5354 2.77 - 3.30: 27106 3.30 - 3.83: 44645 3.83 - 4.37: 50843 4.37 - 4.90: 92142 Nonbonded interactions: 220090 Sorted by model distance: nonbonded pdb=" OH TYR A 537 " pdb=" O GLU A 556 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR F 537 " pdb=" O GLU F 556 " model vdw 2.236 3.040 nonbonded pdb=" O LEU B 69 " pdb=" OH TYR B 74 " model vdw 2.244 3.040 nonbonded pdb=" O LEU E 69 " pdb=" OH TYR E 74 " model vdw 2.244 3.040 nonbonded pdb=" N SER A 333 " pdb=" O SER A 333 " model vdw 2.291 2.496 ... (remaining 220085 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 11.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.320 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1821 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 : 0.006 0.135 30840 Z= 0.332 Angle : 1.370 65.253 41868 Z= 0.894 Chirality : 0.100 2.440 4740 Planarity : 0.008 0.193 5448 Dihedral : 17.250 87.988 11436 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.82 % Favored : 91.81 % Rotamer: Outliers : 1.19 % Allowed : 31.11 % Favored : 67.70 % Cbeta Deviations : 1.40 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.14), residues: 3774 helix: 0.80 (0.16), residues: 1162 sheet: 0.75 (0.23), residues: 640 loop : -2.22 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 348 TYR 0.040 0.002 TYR A 74 PHE 0.021 0.001 PHE F 20 TRP 0.006 0.001 TRP C 182 HIS 0.003 0.001 HIS F 262 Details of bonding type rmsd covalent geometry : bond 0.00552 (30840) covalent geometry : angle 1.36979 (41868) hydrogen bonds : bond 0.14523 ( 1124) hydrogen bonds : angle 5.17599 ( 3084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 0.799 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 40 LEU cc_start: 0.2341 (OUTLIER) cc_final: 0.1701 (pt) REVERT: A 216 GLN cc_start: 0.2485 (mm110) cc_final: 0.2149 (mm-40) REVERT: A 238 PHE cc_start: 0.6446 (t80) cc_final: 0.6069 (t80) REVERT: A 327 VAL cc_start: 0.1824 (p) cc_final: 0.1356 (m) REVERT: A 365 MET cc_start: 0.6229 (ttt) cc_final: 0.5544 (tpt) REVERT: A 435 ASP cc_start: 0.4120 (t0) cc_final: 0.3865 (t0) REVERT: A 482 GLU cc_start: 0.4263 (tp30) cc_final: 0.3457 (mm-30) REVERT: A 603 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7276 (tpt-90) REVERT: A 631 GLU cc_start: 0.4568 (mm-30) cc_final: 0.3564 (mt-10) REVERT: B 46 PHE cc_start: 0.0111 (OUTLIER) cc_final: -0.0658 (m-80) REVERT: B 134 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: B 308 ARG cc_start: 0.2939 (OUTLIER) cc_final: 0.1834 (ttm110) REVERT: B 547 ASN cc_start: 0.3248 (t0) cc_final: 0.2478 (m-40) REVERT: C 188 GLN cc_start: 0.4176 (tt0) cc_final: 0.2723 (tt0) REVERT: C 194 GLN cc_start: 0.5313 (mt0) cc_final: 0.4645 (mm-40) REVERT: C 252 TYR cc_start: 0.4338 (OUTLIER) cc_final: 0.4135 (t80) REVERT: D 188 GLN cc_start: 0.4043 (tt0) cc_final: 0.3561 (tt0) REVERT: D 194 GLN cc_start: 0.5473 (mt0) cc_final: 0.5059 (mp10) REVERT: D 252 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4506 (t80) REVERT: D 315 ARG cc_start: 0.3637 (mtt90) cc_final: 0.2838 (mtm180) REVERT: D 356 MET cc_start: 0.2407 (ptt) cc_final: 0.1083 (mpm) REVERT: D 585 MET cc_start: 0.2635 (mmt) cc_final: 0.2352 (tpp) REVERT: E 110 ARG cc_start: 0.4012 (mtt180) cc_final: 0.2702 (ppp-140) REVERT: E 122 LYS cc_start: 0.4052 (ttmt) cc_final: 0.3465 (ptpt) REVERT: E 308 ARG cc_start: 0.1481 (OUTLIER) cc_final: 0.0472 (mpp-170) REVERT: E 498 ARG cc_start: 0.4348 (mmm-85) cc_final: 0.4002 (tmm160) REVERT: E 505 ASP cc_start: 0.5024 (m-30) cc_final: 0.4414 (p0) REVERT: F 173 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5945 (pp20) REVERT: F 360 ARG cc_start: 0.5319 (mmm-85) cc_final: 0.4143 (tmt170) REVERT: F 622 GLU cc_start: 0.2106 (tt0) cc_final: 0.1572 (mm-30) REVERT: F 631 GLU cc_start: 0.5390 (mm-30) cc_final: 0.5022 (mt-10) outliers start: 39 outliers final: 4 residues processed: 347 average time/residue: 0.6444 time to fit residues: 265.2980 Evaluate side-chains 189 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 252 TYR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 305 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.9980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 175 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN B 366 HIS B 393 ASN B 416 GLN C 225 GLN C 416 GLN D 225 GLN D 416 GLN D 421 HIS E 393 ASN E 416 GLN F 172 ASN F 175 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 343 ASN F 493 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.321300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.311179 restraints weight = 46719.007| |-----------------------------------------------------------------------------| r_work (start): 0.5142 rms_B_bonded: 0.93 r_work: 0.5064 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.5028 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.5028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2457 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 30840 Z= 0.189 Angle : 0.719 10.245 41868 Z= 0.379 Chirality : 0.050 0.314 4740 Planarity : 0.006 0.152 5448 Dihedral : 5.324 54.343 4161 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.90 % Favored : 91.81 % Rotamer: Outliers : 5.45 % Allowed : 26.69 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.04 (0.14), residues: 3774 helix: 0.63 (0.16), residues: 1154 sheet: 0.86 (0.23), residues: 648 loop : -2.16 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 389 TYR 0.032 0.002 TYR E 281 PHE 0.017 0.002 PHE A 46 TRP 0.011 0.001 TRP E 129 HIS 0.013 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00416 (30840) covalent geometry : angle 0.71941 (41868) hydrogen bonds : bond 0.03529 ( 1124) hydrogen bonds : angle 4.53875 ( 3084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 250 time to evaluate : 1.088 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: A 187 MET cc_start: 0.2417 (mmm) cc_final: 0.1750 (mpm) REVERT: A 505 ASP cc_start: 0.5146 (t0) cc_final: 0.4800 (t0) REVERT: B 365 MET cc_start: 0.2424 (OUTLIER) cc_final: 0.0758 (mmm) REVERT: E 102 VAL cc_start: 0.1722 (OUTLIER) cc_final: 0.0382 (t) REVERT: E 122 LYS cc_start: 0.4427 (ttmt) cc_final: 0.4204 (mmtt) REVERT: E 471 THR cc_start: -0.0021 (OUTLIER) cc_final: -0.0600 (t) REVERT: E 591 VAL cc_start: 0.2636 (OUTLIER) cc_final: 0.1745 (t) REVERT: F 11 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.0531 (mmp80) REVERT: F 187 MET cc_start: 0.1965 (mmm) cc_final: 0.1367 (mpp) outliers start: 179 outliers final: 37 residues processed: 395 average time/residue: 0.5504 time to fit residues: 263.6701 Evaluate side-chains 198 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 150 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 96 HIS A 172 ASN A 194 GLN A 343 ASN B 37 GLN B 117 HIS B 343 ASN B 421 HIS C 305 HIS C 366 HIS C 434 ASN C 484 ASN D 305 HIS D 408 HIS D 484 ASN E 262 HIS E 343 ASN E 451 ASN E 459 HIS F 343 ASN F 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.290311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.274453 restraints weight = 39555.222| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 1.06 r_work: 0.4764 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4737 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 30840 Z= 0.308 Angle : 1.055 23.006 41868 Z= 0.553 Chirality : 0.061 0.711 4740 Planarity : 0.009 0.147 5448 Dihedral : 6.212 55.529 4138 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.64 % Favored : 91.04 % Rotamer: Outliers : 7.10 % Allowed : 25.41 % Favored : 67.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.11 (0.13), residues: 3774 helix: -0.60 (0.15), residues: 1132 sheet: 0.35 (0.22), residues: 616 loop : -2.55 (0.12), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 389 TYR 0.038 0.003 TYR C 77 PHE 0.031 0.003 PHE E 154 TRP 0.038 0.003 TRP E 440 HIS 0.020 0.003 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00692 (30840) covalent geometry : angle 1.05467 (41868) hydrogen bonds : bond 0.06513 ( 1124) hydrogen bonds : angle 5.52035 ( 3084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 293 time to evaluate : 1.258 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 537 TYR cc_start: 0.3975 (t80) cc_final: 0.3075 (t80) REVERT: B 184 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: B 482 GLU cc_start: 0.7616 (tt0) cc_final: 0.7288 (tt0) REVERT: B 556 GLU cc_start: 0.7840 (tt0) cc_final: 0.7389 (tm-30) REVERT: C 556 GLU cc_start: 0.7683 (pt0) cc_final: 0.7374 (pp20) REVERT: E 471 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.6347 (p) outliers start: 233 outliers final: 44 residues processed: 486 average time/residue: 0.6163 time to fit residues: 357.4003 Evaluate side-chains 226 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 360 ARG Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 132 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 150 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 393 ASN C 547 ASN D 434 ASN D 547 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.267617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.251282 restraints weight = 36192.742| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 0.84 r_work: 0.4548 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4523 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.4390 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.9987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 30840 Z= 0.190 Angle : 0.736 15.610 41868 Z= 0.385 Chirality : 0.050 0.324 4740 Planarity : 0.006 0.142 5448 Dihedral : 5.128 57.449 4138 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.00 % Favored : 92.71 % Rotamer: Outliers : 3.78 % Allowed : 28.31 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.65 (0.13), residues: 3774 helix: 0.14 (0.15), residues: 1166 sheet: 0.45 (0.22), residues: 634 loop : -2.52 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 389 TYR 0.023 0.002 TYR E 281 PHE 0.020 0.002 PHE F 223 TRP 0.010 0.001 TRP F 131 HIS 0.013 0.002 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00430 (30840) covalent geometry : angle 0.73559 (41868) hydrogen bonds : bond 0.04238 ( 1124) hydrogen bonds : angle 4.62831 ( 3084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 224 time to evaluate : 1.173 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: A 429 ILE cc_start: 0.5949 (OUTLIER) cc_final: 0.5362 (mm) REVERT: A 537 TYR cc_start: 0.4780 (t80) cc_final: 0.3648 (t80) REVERT: A 567 MET cc_start: 0.6902 (mtt) cc_final: 0.6635 (mtt) REVERT: A 574 LEU cc_start: 0.3302 (OUTLIER) cc_final: 0.2638 (mp) REVERT: B 302 ILE cc_start: 0.3804 (OUTLIER) cc_final: 0.3218 (mt) REVERT: B 356 MET cc_start: 0.2154 (mmt) cc_final: 0.1845 (mmp) REVERT: C 26 LYS cc_start: 0.7526 (mtmm) cc_final: 0.7297 (mmmt) REVERT: D 105 ILE cc_start: 0.5332 (OUTLIER) cc_final: 0.4837 (tt) REVERT: D 509 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: D 590 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: E 110 ARG cc_start: 0.4987 (OUTLIER) cc_final: 0.4786 (mtt90) REVERT: E 281 TYR cc_start: 0.2728 (OUTLIER) cc_final: 0.1599 (t80) REVERT: F 440 TRP cc_start: 0.4085 (p-90) cc_final: 0.3282 (p90) outliers start: 124 outliers final: 43 residues processed: 324 average time/residue: 0.6189 time to fit residues: 241.3283 Evaluate side-chains 224 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 609 ARG Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 593 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 24 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 254 optimal weight: 0.0570 chunk 180 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 337 optimal weight: 0.8980 chunk 322 optimal weight: 4.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 411 ASN A 626 GLN B 57 ASN B 194 GLN B 416 GLN C 137 GLN D 484 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.242411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.178872 restraints weight = 33407.051| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 7.63 r_work: 0.3435 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 1.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 30840 Z= 0.230 Angle : 0.880 16.605 41868 Z= 0.462 Chirality : 0.056 0.548 4740 Planarity : 0.007 0.134 5448 Dihedral : 5.537 57.460 4138 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.53 % Favored : 91.15 % Rotamer: Outliers : 4.88 % Allowed : 26.57 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.90 (0.13), residues: 3774 helix: 0.03 (0.15), residues: 1144 sheet: -0.04 (0.22), residues: 668 loop : -2.62 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 308 TYR 0.079 0.003 TYR D 281 PHE 0.027 0.003 PHE B 213 TRP 0.023 0.002 TRP B 440 HIS 0.011 0.002 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00507 (30840) covalent geometry : angle 0.88037 (41868) hydrogen bonds : bond 0.06805 ( 1124) hydrogen bonds : angle 5.05917 ( 3084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 260 time to evaluate : 1.102 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 429 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7031 (mm) REVERT: A 449 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6629 (tt0) REVERT: A 509 MET cc_start: 0.6811 (tpt) cc_final: 0.6100 (ttm) REVERT: A 567 MET cc_start: 0.7537 (mtt) cc_final: 0.7252 (mtt) REVERT: B 302 ILE cc_start: 0.3996 (OUTLIER) cc_final: 0.3281 (mt) REVERT: B 356 MET cc_start: 0.1359 (mmt) cc_final: 0.1069 (mmp) REVERT: B 464 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6585 (tp) REVERT: B 634 THR cc_start: 0.7982 (m) cc_final: 0.7517 (p) REVERT: C 53 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3660 (pt) REVERT: C 79 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.5153 (tm-30) REVERT: C 184 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: C 222 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8556 (mmmt) REVERT: C 233 GLN cc_start: 0.7396 (tt0) cc_final: 0.7154 (mt0) REVERT: C 483 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (mmtp) REVERT: C 509 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (mtt) REVERT: C 556 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7895 (pp20) REVERT: C 590 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: D 102 VAL cc_start: 0.8545 (p) cc_final: 0.8306 (t) REVERT: D 105 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.5242 (tt) REVERT: D 184 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: D 509 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: D 556 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7941 (pp20) REVERT: D 590 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: D 626 GLN cc_start: 0.8429 (mt0) cc_final: 0.8115 (mt0) REVERT: E 302 ILE cc_start: 0.2257 (OUTLIER) cc_final: 0.1535 (mp) REVERT: E 365 MET cc_start: 0.3876 (mpt) cc_final: 0.3493 (mmt) REVERT: E 556 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: E 626 GLN cc_start: 0.7775 (mp10) cc_final: 0.7379 (mm110) REVERT: F 44 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.4905 (m-80) REVERT: F 56 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6356 (mp0) REVERT: F 307 TYR cc_start: 0.4767 (m-80) cc_final: 0.4529 (m-80) REVERT: F 362 ASP cc_start: 0.4830 (OUTLIER) cc_final: 0.3810 (m-30) REVERT: F 414 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6968 (tp) REVERT: F 509 MET cc_start: 0.6721 (tpt) cc_final: 0.6259 (ttm) REVERT: F 521 ARG cc_start: 0.6491 (tpt170) cc_final: 0.6233 (mmt-90) REVERT: F 556 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: F 585 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.3919 (ptm) REVERT: F 626 GLN cc_start: 0.6822 (tp-100) cc_final: 0.5761 (mp10) outliers start: 160 outliers final: 49 residues processed: 391 average time/residue: 0.7617 time to fit residues: 346.0543 Evaluate side-chains 248 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 556 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 362 ASP Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 585 MET Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 90 optimal weight: 9.9990 chunk 231 optimal weight: 0.0870 chunk 211 optimal weight: 0.0570 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 325 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 233 GLN A 408 HIS B 57 ASN C 109 ASN C 225 GLN D 484 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.243342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.184175 restraints weight = 33575.114| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 6.49 r_work: 0.3571 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 1.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 30840 Z= 0.124 Angle : 0.616 8.347 41868 Z= 0.328 Chirality : 0.047 0.264 4740 Planarity : 0.006 0.129 5448 Dihedral : 4.845 58.471 4138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.81 % Favored : 92.90 % Rotamer: Outliers : 2.89 % Allowed : 29.01 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.14), residues: 3774 helix: 0.63 (0.16), residues: 1150 sheet: 0.04 (0.22), residues: 690 loop : -2.45 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.024 0.001 TYR E 281 PHE 0.024 0.001 PHE D 23 TRP 0.008 0.001 TRP D 100 HIS 0.004 0.001 HIS F 305 Details of bonding type rmsd covalent geometry : bond 0.00272 (30840) covalent geometry : angle 0.61645 (41868) hydrogen bonds : bond 0.03891 ( 1124) hydrogen bonds : angle 4.48520 ( 3084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 190 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5398 (tp) REVERT: A 429 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 500 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 509 MET cc_start: 0.6773 (tpt) cc_final: 0.6218 (ttm) REVERT: A 567 MET cc_start: 0.7760 (mtt) cc_final: 0.7535 (mtt) REVERT: B 194 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: B 302 ILE cc_start: 0.4138 (OUTLIER) cc_final: 0.3396 (mt) REVERT: B 634 THR cc_start: 0.7811 (m) cc_final: 0.7470 (p) REVERT: C 53 LEU cc_start: 0.4144 (OUTLIER) cc_final: 0.3864 (tt) REVERT: C 106 GLU cc_start: 0.2627 (OUTLIER) cc_final: 0.2345 (pp20) REVERT: C 556 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: C 590 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: D 27 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: D 92 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: D 102 VAL cc_start: 0.8584 (p) cc_final: 0.8337 (t) REVERT: D 509 MET cc_start: 0.8142 (tpp) cc_final: 0.7742 (mtt) REVERT: D 590 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: E 194 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: E 365 MET cc_start: 0.3786 (mpt) cc_final: 0.3397 (mmt) REVERT: E 626 GLN cc_start: 0.7693 (mp10) cc_final: 0.7362 (mm110) REVERT: F 44 PHE cc_start: 0.5248 (OUTLIER) cc_final: 0.4670 (m-80) REVERT: F 307 TYR cc_start: 0.4923 (m-80) cc_final: 0.4715 (m-80) REVERT: F 414 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7192 (tp) REVERT: F 483 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7504 (ptmt) REVERT: F 585 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.3898 (ptt) outliers start: 95 outliers final: 38 residues processed: 269 average time/residue: 0.6509 time to fit residues: 209.4690 Evaluate side-chains 216 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 585 MET Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 152 optimal weight: 0.3980 chunk 205 optimal weight: 2.9990 chunk 293 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 237 optimal weight: 0.3980 chunk 351 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS D 484 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.236950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173762 restraints weight = 33227.309| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 7.16 r_work: 0.3382 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 1.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 30840 Z= 0.141 Angle : 0.637 10.574 41868 Z= 0.337 Chirality : 0.048 0.229 4740 Planarity : 0.006 0.124 5448 Dihedral : 4.653 57.412 4138 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.53 % Favored : 92.18 % Rotamer: Outliers : 2.99 % Allowed : 29.10 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.14), residues: 3774 helix: 0.87 (0.16), residues: 1144 sheet: 0.37 (0.22), residues: 664 loop : -2.39 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 11 TYR 0.041 0.002 TYR E 281 PHE 0.024 0.002 PHE C 23 TRP 0.012 0.001 TRP E 440 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00319 (30840) covalent geometry : angle 0.63721 (41868) hydrogen bonds : bond 0.04420 ( 1124) hydrogen bonds : angle 4.24012 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 197 time to evaluate : 1.207 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 108 ILE cc_start: 0.2924 (OUTLIER) cc_final: 0.2257 (tp) REVERT: A 362 ASP cc_start: 0.5095 (OUTLIER) cc_final: 0.3491 (t70) REVERT: A 365 MET cc_start: 0.3836 (mtp) cc_final: 0.3597 (mtp) REVERT: A 380 ILE cc_start: 0.0158 (OUTLIER) cc_final: -0.0252 (pt) REVERT: A 429 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7015 (mm) REVERT: A 509 MET cc_start: 0.6922 (tpt) cc_final: 0.6386 (ttm) REVERT: A 556 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.5568 (tm-30) REVERT: B 93 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.5107 (mmt) REVERT: B 194 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8059 (mm-40) REVERT: B 302 ILE cc_start: 0.4091 (OUTLIER) cc_final: 0.3362 (mt) REVERT: B 356 MET cc_start: 0.1819 (mmm) cc_final: 0.1548 (mmt) REVERT: B 461 LYS cc_start: 0.7788 (mmtp) cc_final: 0.6691 (mtmp) REVERT: B 464 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6996 (tp) REVERT: B 483 LYS cc_start: 0.7875 (tptt) cc_final: 0.7569 (tptt) REVERT: B 567 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8239 (ptm) REVERT: B 634 THR cc_start: 0.7835 (m) cc_final: 0.7470 (p) REVERT: C 53 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.3994 (tt) REVERT: C 556 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7694 (pp20) REVERT: C 590 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: D 92 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: D 509 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: D 556 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: D 590 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: E 365 MET cc_start: 0.3781 (mpt) cc_final: 0.2962 (mmt) REVERT: E 513 ASP cc_start: 0.8388 (p0) cc_final: 0.8171 (p0) REVERT: E 604 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: E 626 GLN cc_start: 0.7799 (mp10) cc_final: 0.7479 (mm110) REVERT: E 634 THR cc_start: 0.8022 (m) cc_final: 0.7603 (p) REVERT: F 44 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4674 (m-10) REVERT: F 105 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4518 (tp) REVERT: F 421 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.5792 (t70) REVERT: F 483 LYS cc_start: 0.8057 (mmtp) cc_final: 0.7335 (ptmt) outliers start: 98 outliers final: 41 residues processed: 279 average time/residue: 0.6963 time to fit residues: 229.6138 Evaluate side-chains 227 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 253 optimal weight: 0.9990 chunk 343 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 299 optimal weight: 0.4980 chunk 32 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 57 ASN B 393 ASN B 416 GLN B 536 HIS D 109 ASN D 137 GLN E 27 GLN F 501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.230111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166228 restraints weight = 32604.789| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 6.96 r_work: 0.3296 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 1.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 30840 Z= 0.169 Angle : 0.685 13.704 41868 Z= 0.362 Chirality : 0.053 1.154 4740 Planarity : 0.006 0.121 5448 Dihedral : 4.819 56.377 4138 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.92 % Favored : 92.77 % Rotamer: Outliers : 2.93 % Allowed : 29.40 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.14), residues: 3774 helix: 0.78 (0.16), residues: 1146 sheet: 0.29 (0.22), residues: 674 loop : -2.36 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 308 TYR 0.038 0.002 TYR E 281 PHE 0.022 0.002 PHE D 44 TRP 0.011 0.001 TRP E 440 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00383 (30840) covalent geometry : angle 0.68468 (41868) hydrogen bonds : bond 0.05096 ( 1124) hydrogen bonds : angle 4.31752 ( 3084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 189 time to evaluate : 1.266 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 315 ARG cc_start: 0.6885 (mmt90) cc_final: 0.6559 (mmm160) REVERT: A 429 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7326 (mm) REVERT: A 509 MET cc_start: 0.7290 (tpt) cc_final: 0.6752 (mtp) REVERT: A 626 GLN cc_start: 0.6681 (tp40) cc_final: 0.5509 (mp10) REVERT: B 93 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5718 (mtt) REVERT: B 194 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.7940 (mm-40) REVERT: B 302 ILE cc_start: 0.3965 (OUTLIER) cc_final: 0.3192 (mt) REVERT: B 461 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7515 (mtpt) REVERT: B 464 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7652 (tp) REVERT: B 509 MET cc_start: 0.8059 (ptp) cc_final: 0.7854 (mtm) REVERT: C 53 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.4207 (tt) REVERT: C 365 MET cc_start: 0.5542 (ptm) cc_final: 0.5296 (ttp) REVERT: C 509 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7600 (mtt) REVERT: C 556 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7774 (pp20) REVERT: C 590 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: D 92 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: D 509 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7747 (mtt) REVERT: D 556 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: D 590 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: E 194 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: E 302 ILE cc_start: 0.2357 (OUTLIER) cc_final: 0.1495 (mp) REVERT: E 306 ASP cc_start: 0.7749 (m-30) cc_final: 0.7432 (m-30) REVERT: E 365 MET cc_start: 0.3955 (mpt) cc_final: 0.2928 (mmt) REVERT: E 604 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: E 634 THR cc_start: 0.8041 (m) cc_final: 0.7716 (p) REVERT: F 29 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6964 (m) REVERT: F 44 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.4629 (m-10) REVERT: F 119 ARG cc_start: 0.6180 (ttp80) cc_final: 0.5690 (ttp80) REVERT: F 421 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6000 (t70) REVERT: F 483 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7308 (ptmt) REVERT: F 494 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7949 (tpp-160) REVERT: F 599 ILE cc_start: 0.4511 (OUTLIER) cc_final: 0.3809 (tp) outliers start: 96 outliers final: 40 residues processed: 269 average time/residue: 0.7751 time to fit residues: 242.8375 Evaluate side-chains 229 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 ILE Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 172 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 157 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 90 optimal weight: 30.0000 chunk 256 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS B 57 ASN B 151 GLN B 536 HIS C 225 GLN C 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.231911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169125 restraints weight = 32745.896| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 6.73 r_work: 0.3343 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 1.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30840 Z= 0.117 Angle : 0.590 9.858 41868 Z= 0.312 Chirality : 0.046 0.203 4740 Planarity : 0.005 0.117 5448 Dihedral : 4.513 56.573 4138 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.06 % Rotamer: Outliers : 2.16 % Allowed : 30.20 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.14), residues: 3774 helix: 0.98 (0.16), residues: 1152 sheet: 0.44 (0.22), residues: 680 loop : -2.34 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 119 TYR 0.028 0.001 TYR B 457 PHE 0.017 0.001 PHE C 399 TRP 0.012 0.001 TRP E 129 HIS 0.024 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00258 (30840) covalent geometry : angle 0.58969 (41868) hydrogen bonds : bond 0.03797 ( 1124) hydrogen bonds : angle 4.12675 ( 3084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 1.249 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 315 ARG cc_start: 0.6831 (mmt90) cc_final: 0.6541 (mmm160) REVERT: A 380 ILE cc_start: 0.0147 (OUTLIER) cc_final: -0.0240 (pt) REVERT: A 429 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7231 (mm) REVERT: A 483 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7120 (tmtt) REVERT: A 494 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.7216 (tpp-160) REVERT: A 509 MET cc_start: 0.7139 (tpt) cc_final: 0.6691 (mtp) REVERT: A 626 GLN cc_start: 0.6763 (tp40) cc_final: 0.5983 (mp10) REVERT: A 630 LYS cc_start: 0.7575 (pmtt) cc_final: 0.7302 (mptt) REVERT: B 194 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7971 (mm-40) REVERT: B 302 ILE cc_start: 0.3994 (OUTLIER) cc_final: 0.3171 (mt) REVERT: B 461 LYS cc_start: 0.8413 (mmtp) cc_final: 0.7652 (mtpt) REVERT: B 464 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7600 (tp) REVERT: B 483 LYS cc_start: 0.7825 (tptt) cc_final: 0.7538 (tptt) REVERT: C 53 LEU cc_start: 0.4643 (OUTLIER) cc_final: 0.4397 (tt) REVERT: C 590 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: D 509 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7705 (mtt) REVERT: D 535 ARG cc_start: 0.7897 (ptm-80) cc_final: 0.7693 (pmm150) REVERT: D 556 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: D 590 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: E 302 ILE cc_start: 0.2395 (OUTLIER) cc_final: 0.1508 (mp) REVERT: E 306 ASP cc_start: 0.7645 (m-30) cc_final: 0.7344 (m-30) REVERT: E 365 MET cc_start: 0.3784 (mpt) cc_final: 0.3248 (mmt) REVERT: E 461 LYS cc_start: 0.7783 (mmtp) cc_final: 0.6698 (ptpp) REVERT: E 604 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: F 29 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6888 (m) REVERT: F 42 PHE cc_start: 0.5184 (p90) cc_final: 0.4944 (p90) REVERT: F 44 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4720 (m-10) REVERT: F 105 ILE cc_start: 0.5416 (OUTLIER) cc_final: 0.4944 (tp) REVERT: F 119 ARG cc_start: 0.6137 (ttp80) cc_final: 0.5617 (ttp80) REVERT: F 315 ARG cc_start: 0.7061 (mpt-90) cc_final: 0.6446 (mmp-170) REVERT: F 483 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7356 (ptmt) REVERT: F 494 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7946 (tpp-160) REVERT: F 599 ILE cc_start: 0.4502 (OUTLIER) cc_final: 0.3802 (tp) outliers start: 71 outliers final: 27 residues processed: 241 average time/residue: 0.7656 time to fit residues: 215.4343 Evaluate side-chains 215 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 ILE Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 162 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 196 optimal weight: 0.0370 chunk 210 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 175 HIS B 57 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.227693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162783 restraints weight = 32486.305| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 7.21 r_work: 0.3256 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 1.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 30840 Z= 0.140 Angle : 0.659 13.264 41868 Z= 0.344 Chirality : 0.048 0.214 4740 Planarity : 0.006 0.115 5448 Dihedral : 4.563 56.152 4138 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.21 % Favored : 92.47 % Rotamer: Outliers : 1.74 % Allowed : 30.59 % Favored : 67.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.14), residues: 3774 helix: 0.83 (0.16), residues: 1196 sheet: 0.43 (0.22), residues: 686 loop : -2.36 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 110 TYR 0.022 0.002 TYR C 387 PHE 0.019 0.002 PHE E 568 TRP 0.015 0.001 TRP E 129 HIS 0.009 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00320 (30840) covalent geometry : angle 0.65855 (41868) hydrogen bonds : bond 0.04702 ( 1124) hydrogen bonds : angle 4.11344 ( 3084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 1.178 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 315 ARG cc_start: 0.6851 (mmt90) cc_final: 0.6454 (mmm160) REVERT: A 429 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7316 (mm) REVERT: A 483 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7222 (ptmt) REVERT: A 494 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7155 (tpp-160) REVERT: A 509 MET cc_start: 0.7255 (tpt) cc_final: 0.6811 (mtp) REVERT: A 626 GLN cc_start: 0.7094 (tp40) cc_final: 0.6201 (mp10) REVERT: A 630 LYS cc_start: 0.7937 (pmtt) cc_final: 0.7576 (mptt) REVERT: B 194 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: B 302 ILE cc_start: 0.3820 (OUTLIER) cc_final: 0.3330 (mt) REVERT: B 431 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8446 (pt) REVERT: B 464 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (tp) REVERT: B 483 LYS cc_start: 0.7936 (tptt) cc_final: 0.7641 (tptt) REVERT: C 53 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4444 (tt) REVERT: C 509 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: C 582 GLU cc_start: 0.7751 (tt0) cc_final: 0.7503 (tm-30) REVERT: C 590 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: D 509 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7718 (mtt) REVERT: D 556 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7776 (pp20) REVERT: D 590 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: E 302 ILE cc_start: 0.2370 (OUTLIER) cc_final: 0.1371 (mp) REVERT: E 306 ASP cc_start: 0.8112 (m-30) cc_final: 0.7825 (m-30) REVERT: E 483 LYS cc_start: 0.7943 (tptt) cc_final: 0.7724 (tptt) REVERT: E 604 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: F 29 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6808 (m) REVERT: F 105 ILE cc_start: 0.5566 (OUTLIER) cc_final: 0.5155 (tp) REVERT: F 119 ARG cc_start: 0.6439 (ttp80) cc_final: 0.5817 (ttp-170) REVERT: F 315 ARG cc_start: 0.7098 (mpt-90) cc_final: 0.6516 (mmm160) REVERT: F 483 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7359 (ptmt) REVERT: F 494 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7951 (tpp-160) REVERT: F 599 ILE cc_start: 0.4620 (OUTLIER) cc_final: 0.3933 (tp) REVERT: F 630 LYS cc_start: 0.7897 (mptt) cc_final: 0.7622 (pmtt) outliers start: 57 outliers final: 32 residues processed: 236 average time/residue: 0.7860 time to fit residues: 215.5487 Evaluate side-chains 219 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 ILE Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 350 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 322 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 315 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 175 HIS ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 175 HIS F 573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.222180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156869 restraints weight = 32341.175| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 7.34 r_work: 0.3153 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 1.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 30840 Z= 0.187 Angle : 0.719 11.792 41868 Z= 0.381 Chirality : 0.050 0.237 4740 Planarity : 0.006 0.113 5448 Dihedral : 4.931 55.497 4138 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.37 % Favored : 92.26 % Rotamer: Outliers : 1.89 % Allowed : 30.65 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.14), residues: 3774 helix: 0.76 (0.16), residues: 1154 sheet: 0.42 (0.22), residues: 640 loop : -2.44 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 155 TYR 0.033 0.002 TYR E 126 PHE 0.031 0.002 PHE E 568 TRP 0.022 0.002 TRP E 129 HIS 0.019 0.002 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00430 (30840) covalent geometry : angle 0.71898 (41868) hydrogen bonds : bond 0.05771 ( 1124) hydrogen bonds : angle 4.33778 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11339.80 seconds wall clock time: 194 minutes 4.52 seconds (11644.52 seconds total)