Starting phenix.real_space_refine on Wed May 28 05:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxh_29533/05_2025/8fxh_29533_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxh_29533/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxh_29533/05_2025/8fxh_29533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxh_29533/05_2025/8fxh_29533.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxh_29533/05_2025/8fxh_29533_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxh_29533/05_2025/8fxh_29533_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.47, per 1000 atoms: 0.68 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: 7.43 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.90 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: 11.67 Time building geometry restraints manager: 8.76 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: 0.05 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: 14.000 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: 0.000 Extract box with map and model: 1.720 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 69.310 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.040 ------------------------------------------------------------------------------- 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 : 6.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP C 182 HIS 0.003 0.001 HIS F 262 PHE 0.021 0.001 PHE F 20 TYR 0.040 0.002 TYR A 74 ARG 0.013 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.14523 ( 1124) hydrogen bonds : angle 5.17599 ( 3084) covalent geometry : bond 0.00552 (30840) covalent geometry : angle 1.36979 (41868) *********************** 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 : 2.949 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: 1.2607 time to fit residues: 521.6208 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 : 2.726 ------------------------------------------------------------------------------- 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 319 optimal weight: 30.0000 chunk 286 optimal weight: 0.0370 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 193 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 296 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 220 optimal weight: 0.0970 chunk 343 optimal weight: 1.9990 overall best weight: 0.0972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN B 366 HIS B 416 GLN C 416 GLN D 225 GLN D 416 GLN D 421 HIS E 416 GLN E 420 GLN E 459 HIS F 172 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.327913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.320686 restraints weight = 47733.714| |-----------------------------------------------------------------------------| r_work (start): 0.5209 rms_B_bonded: 0.98 r_work: 0.5147 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.5102 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.5102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1402 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 30840 Z= 0.132 Angle : 0.639 11.332 41868 Z= 0.335 Chirality : 0.046 0.215 4740 Planarity : 0.006 0.156 5448 Dihedral : 5.193 52.236 4161 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.02 % Favored : 92.63 % Rotamer: Outliers : 3.66 % Allowed : 28.37 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3774 helix: 0.90 (0.16), residues: 1174 sheet: 0.88 (0.23), residues: 652 loop : -2.14 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.013 0.001 HIS D 366 PHE 0.015 0.001 PHE A 46 TYR 0.025 0.001 TYR E 281 ARG 0.006 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1124) hydrogen bonds : angle 4.51323 ( 3084) covalent geometry : bond 0.00290 (30840) covalent geometry : angle 0.63857 (41868) *********************** 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 323 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 203 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.1764 (mmm) cc_final: 0.0821 (mpm) REVERT: B 46 PHE cc_start: -0.0241 (OUTLIER) cc_final: -0.1071 (m-80) REVERT: B 102 VAL cc_start: 0.4008 (OUTLIER) cc_final: 0.3041 (t) REVERT: B 547 ASN cc_start: 0.2875 (t0) cc_final: 0.2500 (m110) REVERT: C 356 MET cc_start: 0.3390 (OUTLIER) cc_final: 0.0139 (mpm) REVERT: E 102 VAL cc_start: 0.1382 (OUTLIER) cc_final: 0.0005 (t) REVERT: E 585 MET cc_start: 0.3369 (OUTLIER) cc_final: 0.2764 (ttt) REVERT: F 11 ARG cc_start: 0.3257 (OUTLIER) cc_final: 0.2337 (mtm110) REVERT: F 187 MET cc_start: 0.1491 (mmm) cc_final: 0.0881 (mpp) outliers start: 120 outliers final: 32 residues processed: 300 average time/residue: 1.1069 time to fit residues: 406.7201 Evaluate side-chains 197 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 227 LEU 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 D residue 586 ILE Chi-restraints excluded: chain D residue 590 ASP 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 194 GLN Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 305 HIS Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 585 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.0010 chunk 292 optimal weight: 0.8980 chunk 203 optimal weight: 0.5980 chunk 307 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 242 optimal weight: 0.1980 chunk 232 optimal weight: 0.0470 chunk 181 optimal weight: 0.8980 chunk 347 optimal weight: 9.9990 chunk 262 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS B 37 GLN B 262 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN E 27 GLN E 37 GLN E 262 HIS F 175 HIS F 343 ASN F 573 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.321321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.311551 restraints weight = 46578.591| |-----------------------------------------------------------------------------| r_work (start): 0.5150 rms_B_bonded: 1.16 r_work: 0.5068 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.5021 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.5021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2466 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 30840 Z= 0.151 Angle : 0.625 12.069 41868 Z= 0.325 Chirality : 0.047 0.295 4740 Planarity : 0.006 0.146 5448 Dihedral : 4.657 50.276 4140 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.02 % Favored : 92.71 % Rotamer: Outliers : 3.90 % Allowed : 27.67 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3774 helix: 1.02 (0.16), residues: 1128 sheet: 0.95 (0.23), residues: 648 loop : -2.03 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 129 HIS 0.007 0.001 HIS E 118 PHE 0.013 0.001 PHE E 203 TYR 0.033 0.001 TYR A 66 ARG 0.018 0.001 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 1124) hydrogen bonds : angle 4.37505 ( 3084) covalent geometry : bond 0.00322 (30840) covalent geometry : angle 0.62548 (41868) *********************** 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 344 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 216 time to evaluate : 3.317 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 187 MET cc_start: 0.2478 (mmm) cc_final: 0.1405 (mpm) REVERT: B 22 ILE cc_start: 0.3292 (OUTLIER) cc_final: 0.2878 (mt) REVERT: B 356 MET cc_start: 0.2417 (mpm) cc_final: 0.2034 (mpt) REVERT: B 365 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.0656 (mmm) REVERT: E 102 VAL cc_start: 0.1666 (OUTLIER) cc_final: 0.0466 (t) REVERT: E 471 THR cc_start: 0.0230 (OUTLIER) cc_final: -0.0310 (m) REVERT: E 475 LEU cc_start: 0.2021 (OUTLIER) cc_final: 0.1110 (tp) REVERT: E 547 ASN cc_start: 0.3506 (t0) cc_final: 0.3037 (m110) REVERT: E 552 LEU cc_start: -0.0070 (OUTLIER) cc_final: -0.0582 (tt) REVERT: E 591 VAL cc_start: 0.2566 (OUTLIER) cc_final: 0.1954 (t) REVERT: F 458 MET cc_start: 0.0442 (pmt) cc_final: 0.0230 (pmm) outliers start: 128 outliers final: 41 residues processed: 323 average time/residue: 1.0950 time to fit residues: 434.2088 Evaluate side-chains 187 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 PHE 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 510 SER Chi-restraints excluded: chain D residue 93 MET 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 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 471 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 290 LEU 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 500 LEU 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 264 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 343 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 160 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 89 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS C 305 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 305 HIS D 408 HIS ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN E 194 GLN E 421 HIS E 451 ASN F 343 ASN F 393 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.294267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.278173 restraints weight = 40226.037| |-----------------------------------------------------------------------------| r_work (start): 0.4904 rms_B_bonded: 1.10 r_work: 0.4798 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4775 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.8241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.187 30840 Z= 0.282 Angle : 0.991 25.837 41868 Z= 0.513 Chirality : 0.058 0.513 4740 Planarity : 0.008 0.139 5448 Dihedral : 5.667 50.960 4138 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.45 % Favored : 91.18 % Rotamer: Outliers : 5.39 % Allowed : 27.33 % Favored : 67.28 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3774 helix: -0.36 (0.15), residues: 1148 sheet: 0.53 (0.22), residues: 606 loop : -2.47 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 440 HIS 0.011 0.002 HIS B 408 PHE 0.158 0.003 PHE F 44 TYR 0.048 0.003 TYR A 368 ARG 0.017 0.001 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.05492 ( 1124) hydrogen bonds : angle 5.15996 ( 3084) covalent geometry : bond 0.00627 (30840) covalent geometry : angle 0.99127 (41868) *********************** 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 461 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 284 time to evaluate : 2.947 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 447 ILE cc_start: 0.2790 (OUTLIER) cc_final: 0.2582 (tt) REVERT: A 537 TYR cc_start: 0.3683 (t80) cc_final: 0.2830 (t80) REVERT: B 356 MET cc_start: 0.2706 (mpm) cc_final: 0.2379 (mpt) REVERT: B 471 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6389 (p) REVERT: B 556 GLU cc_start: 0.7813 (tt0) cc_final: 0.7424 (tm-30) REVERT: C 556 GLU cc_start: 0.7417 (pt0) cc_final: 0.6927 (pp20) REVERT: D 105 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.3934 (mp) REVERT: D 204 ASP cc_start: 0.7767 (p0) cc_final: 0.7546 (p0) REVERT: D 556 GLU cc_start: 0.7665 (pt0) cc_final: 0.6958 (pp20) REVERT: E 471 THR cc_start: 0.5933 (OUTLIER) cc_final: 0.5533 (p) REVERT: F 11 ARG cc_start: 0.3290 (OUTLIER) cc_final: 0.0742 (mmp80) REVERT: F 105 ILE cc_start: 0.4038 (OUTLIER) cc_final: 0.3755 (tp) REVERT: F 317 VAL cc_start: 0.3503 (OUTLIER) cc_final: 0.3194 (m) outliers start: 177 outliers final: 42 residues processed: 425 average time/residue: 1.2451 time to fit residues: 632.2041 Evaluate side-chains 215 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 447 ILE 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 302 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 497 ILE 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 105 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 317 VAL 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 432 ILE Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 192 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 296 optimal weight: 0.0980 chunk 210 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 256 optimal weight: 0.9990 chunk 347 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 547 ASN D 37 GLN D 172 ASN D 434 ASN D 547 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 152 GLN F 343 ASN F 459 HIS F 573 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.272029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.253706 restraints weight = 36774.432| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 1.03 r_work: 0.4575 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4549 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.9635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30840 Z= 0.172 Angle : 0.723 17.808 41868 Z= 0.374 Chirality : 0.049 0.233 4740 Planarity : 0.006 0.137 5448 Dihedral : 4.928 52.094 4138 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.68 % Favored : 93.03 % Rotamer: Outliers : 3.50 % Allowed : 28.64 % Favored : 67.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3774 helix: 0.48 (0.15), residues: 1152 sheet: 0.17 (0.22), residues: 672 loop : -2.22 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 440 HIS 0.007 0.001 HIS E 117 PHE 0.031 0.002 PHE F 44 TYR 0.047 0.002 TYR B 281 ARG 0.015 0.001 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1124) hydrogen bonds : angle 4.48635 ( 3084) covalent geometry : bond 0.00381 (30840) covalent geometry : angle 0.72269 (41868) *********************** 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 351 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 236 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5027 (mm) REVERT: B 302 ILE cc_start: 0.3657 (OUTLIER) cc_final: 0.3223 (mt) REVERT: C 26 LYS cc_start: 0.7157 (mtmm) cc_final: 0.6891 (mmmt) REVERT: D 105 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4660 (tt) REVERT: D 590 ASP cc_start: 0.6869 (p0) cc_final: 0.6557 (m-30) REVERT: E 194 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: F 440 TRP cc_start: 0.3487 (p-90) cc_final: 0.2979 (p90) outliers start: 115 outliers final: 42 residues processed: 327 average time/residue: 1.1867 time to fit residues: 467.3423 Evaluate side-chains 211 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 3.337 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 481 THR 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 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 C residue 27 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 201 THR 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 526 ILE Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain F residue 25 VAL 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 199 ILE Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 575 VAL 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 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 40.0000 chunk 272 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 90 optimal weight: 40.0000 chunk 130 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 484 ASN C 615 GLN D 37 GLN ** 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 = 0.4730 r_free = 0.4730 target = 0.256215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.235786 restraints weight = 34904.235| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 0.98 r_work: 0.4408 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.4379 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 1.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 30840 Z= 0.182 Angle : 0.733 20.932 41868 Z= 0.380 Chirality : 0.050 0.374 4740 Planarity : 0.006 0.127 5448 Dihedral : 4.848 52.424 4138 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.74 % Favored : 91.94 % Rotamer: Outliers : 3.50 % Allowed : 29.34 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3774 helix: 0.45 (0.15), residues: 1172 sheet: 0.22 (0.22), residues: 666 loop : -2.33 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 440 HIS 0.028 0.002 HIS B 118 PHE 0.031 0.002 PHE E 44 TYR 0.050 0.002 TYR B 281 ARG 0.017 0.001 ARG F 315 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 1124) hydrogen bonds : angle 4.49702 ( 3084) covalent geometry : bond 0.00396 (30840) covalent geometry : angle 0.73260 (41868) *********************** 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 328 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 213 time to evaluate : 3.137 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 380 ILE cc_start: -0.0960 (OUTLIER) cc_final: -0.1285 (pt) REVERT: A 429 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6340 (mm) REVERT: B 302 ILE cc_start: 0.3699 (OUTLIER) cc_final: 0.3250 (mt) REVERT: B 578 GLU cc_start: 0.7640 (tt0) cc_final: 0.7413 (tt0) REVERT: C 187 MET cc_start: 0.8710 (mmt) cc_final: 0.8470 (tpt) REVERT: C 194 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: C 444 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7241 (m) REVERT: C 458 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6365 (mpt) REVERT: C 590 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: D 105 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4754 (tt) REVERT: D 187 MET cc_start: 0.8741 (mmt) cc_final: 0.8485 (tpt) REVERT: D 406 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7906 (mtm-85) REVERT: D 509 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: D 556 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: E 194 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: F 440 TRP cc_start: 0.4833 (p-90) cc_final: 0.4502 (p-90) REVERT: F 585 MET cc_start: 0.4349 (mmp) cc_final: 0.3999 (ptm) outliers start: 115 outliers final: 36 residues processed: 307 average time/residue: 1.2940 time to fit residues: 483.1923 Evaluate side-chains 216 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 3.308 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 575 VAL 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 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 C residue 194 GLN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 LYS 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 432 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 549 LYS Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 316 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 377 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 359 optimal weight: 0.5980 chunk 339 optimal weight: 10.0000 chunk 182 optimal weight: 0.0770 chunk 247 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 278 optimal weight: 50.0000 chunk 225 optimal weight: 9.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 172 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 408 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 434 ASN C 615 GLN D 37 GLN D 137 GLN D 233 GLN D 484 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 172 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.243885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.185465 restraints weight = 33410.973| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 6.43 r_work: 0.3558 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 1.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 30840 Z= 0.184 Angle : 0.728 18.138 41868 Z= 0.378 Chirality : 0.051 0.517 4740 Planarity : 0.006 0.125 5448 Dihedral : 4.799 55.025 4136 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.86 % Favored : 92.74 % Rotamer: Outliers : 3.26 % Allowed : 29.65 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3774 helix: 0.91 (0.16), residues: 1124 sheet: 0.23 (0.22), residues: 670 loop : -2.32 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 440 HIS 0.022 0.001 HIS A 366 PHE 0.028 0.002 PHE F 445 TYR 0.032 0.002 TYR B 281 ARG 0.014 0.001 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1124) hydrogen bonds : angle 4.46541 ( 3084) covalent geometry : bond 0.00402 (30840) covalent geometry : angle 0.72804 (41868) *********************** 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 335 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 228 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.2936 (OUTLIER) cc_final: 0.2732 (tp) REVERT: A 429 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.6877 (mm) REVERT: B 93 MET cc_start: 0.4773 (tpp) cc_final: 0.4432 (mmt) REVERT: B 464 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6585 (tp) REVERT: B 560 ASP cc_start: 0.7259 (m-30) cc_final: 0.6972 (m-30) REVERT: B 634 THR cc_start: 0.7766 (m) cc_final: 0.7337 (p) REVERT: C 187 MET cc_start: 0.8626 (mmt) cc_final: 0.8371 (tpp) REVERT: C 194 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8158 (mm-40) REVERT: C 444 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7884 (m) REVERT: C 556 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: C 560 ASP cc_start: 0.8208 (m-30) cc_final: 0.7992 (m-30) REVERT: C 590 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: D 187 MET cc_start: 0.8618 (mmt) cc_final: 0.8350 (tpp) REVERT: D 509 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7812 (mtt) REVERT: D 626 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7957 (mp10) REVERT: E 194 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: E 365 MET cc_start: 0.2946 (mmm) cc_final: 0.1232 (mpt) REVERT: E 431 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7091 (tt) REVERT: F 37 GLN cc_start: 0.8077 (mp10) cc_final: 0.7790 (mp10) REVERT: F 44 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4179 (m-10) REVERT: F 56 GLU cc_start: 0.6462 (mm-30) cc_final: 0.6138 (mp0) REVERT: F 105 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4405 (tp) REVERT: F 307 TYR cc_start: 0.4864 (m-80) cc_final: 0.4617 (m-80) REVERT: F 483 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7399 (ptmt) REVERT: F 585 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.3472 (ptt) REVERT: F 626 GLN cc_start: 0.6697 (tp-100) cc_final: 0.6434 (mp10) outliers start: 107 outliers final: 30 residues processed: 311 average time/residue: 1.3204 time to fit residues: 487.7085 Evaluate side-chains 211 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 3.335 ------------------------------------------------------------------------------- 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 150 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 127 CYS 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 C residue 194 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 201 THR 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 E residue 46 PHE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 495 VAL 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 105 ILE Chi-restraints excluded: chain F residue 124 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 285 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 575 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 26 optimal weight: 0.9990 chunk 317 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 359 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 109 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.238872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.177206 restraints weight = 33221.297| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 6.97 r_work: 0.3445 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 1.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 30840 Z= 0.147 Angle : 0.662 20.441 41868 Z= 0.343 Chirality : 0.048 0.260 4740 Planarity : 0.005 0.118 5448 Dihedral : 4.552 55.574 4136 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.42 % Favored : 92.18 % Rotamer: Outliers : 2.01 % Allowed : 30.68 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3774 helix: 1.01 (0.16), residues: 1140 sheet: 0.34 (0.22), residues: 662 loop : -2.30 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.005 0.001 HIS E 96 PHE 0.029 0.002 PHE F 445 TYR 0.036 0.002 TYR B 281 ARG 0.008 0.001 ARG F 473 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 1124) hydrogen bonds : angle 4.23846 ( 3084) covalent geometry : bond 0.00330 (30840) covalent geometry : angle 0.66218 (41868) *********************** 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 251 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.2202 (OUTLIER) cc_final: 0.1963 (tp) REVERT: A 429 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 585 MET cc_start: 0.4830 (mmt) cc_final: 0.4540 (mmm) REVERT: B 461 LYS cc_start: 0.7755 (mmtp) cc_final: 0.6759 (mtmp) REVERT: B 464 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6958 (tp) REVERT: B 483 LYS cc_start: 0.7910 (tptt) cc_final: 0.7674 (tptt) REVERT: B 509 MET cc_start: 0.7936 (ptp) cc_final: 0.7698 (mtm) REVERT: C 187 MET cc_start: 0.8746 (mmt) cc_final: 0.8430 (tpp) REVERT: C 194 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8146 (mm-40) REVERT: C 509 MET cc_start: 0.8124 (tpp) cc_final: 0.7672 (mtt) REVERT: C 556 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: C 590 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: C 604 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7835 (mm-30) REVERT: D 187 MET cc_start: 0.8735 (mmt) cc_final: 0.8474 (tpp) REVERT: D 509 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7885 (mtt) REVERT: D 556 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: D 626 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: E 123 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5862 (mt-10) REVERT: E 194 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: E 634 THR cc_start: 0.7897 (m) cc_final: 0.7484 (p) REVERT: F 37 GLN cc_start: 0.8113 (mp10) cc_final: 0.7767 (mp10) REVERT: F 44 PHE cc_start: 0.4894 (OUTLIER) cc_final: 0.4121 (m-10) REVERT: F 105 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4544 (tp) REVERT: F 307 TYR cc_start: 0.5036 (m-80) cc_final: 0.4796 (m-80) REVERT: F 483 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7362 (ptmt) REVERT: F 626 GLN cc_start: 0.6851 (tp-100) cc_final: 0.6018 (mp10) outliers start: 66 outliers final: 36 residues processed: 238 average time/residue: 1.3789 time to fit residues: 392.2770 Evaluate side-chains 205 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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 147 ILE 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 449 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 127 CYS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 194 GLN 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 43 ASP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 626 GLN Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 194 GLN 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 567 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 40 LEU 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 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 504 SER Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 148 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 HIS C 109 ASN D 109 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.237145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175627 restraints weight = 33026.911| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 6.86 r_work: 0.3437 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 1.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 30840 Z= 0.145 Angle : 0.646 18.415 41868 Z= 0.337 Chirality : 0.047 0.233 4740 Planarity : 0.005 0.117 5448 Dihedral : 4.482 55.526 4136 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.92 % Favored : 92.69 % Rotamer: Outliers : 1.92 % Allowed : 30.99 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3774 helix: 1.08 (0.16), residues: 1142 sheet: 0.43 (0.22), residues: 656 loop : -2.32 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.006 0.001 HIS B 536 PHE 0.035 0.002 PHE D 42 TYR 0.034 0.002 TYR B 281 ARG 0.008 0.000 ARG F 473 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1124) hydrogen bonds : angle 4.18866 ( 3084) covalent geometry : bond 0.00327 (30840) covalent geometry : angle 0.64587 (41868) *********************** 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 249 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 3.078 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 429 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7179 (mm) REVERT: A 585 MET cc_start: 0.5031 (mmt) cc_final: 0.4716 (mmm) REVERT: B 461 LYS cc_start: 0.7972 (mmtp) cc_final: 0.6946 (mtmp) REVERT: B 464 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7175 (tp) REVERT: B 483 LYS cc_start: 0.7905 (tptt) cc_final: 0.7677 (tptt) REVERT: C 187 MET cc_start: 0.8738 (mmt) cc_final: 0.8372 (tpp) REVERT: C 194 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: C 509 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7696 (mtt) REVERT: C 556 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7707 (pp20) REVERT: C 590 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: C 604 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7824 (mm-30) REVERT: D 187 MET cc_start: 0.8732 (mmt) cc_final: 0.8460 (tpp) REVERT: D 509 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (mtt) REVERT: D 556 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: D 626 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: E 123 GLU cc_start: 0.6316 (tm-30) cc_final: 0.5741 (mp0) REVERT: E 194 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: E 634 THR cc_start: 0.7929 (m) cc_final: 0.7597 (p) REVERT: F 44 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4190 (m-10) REVERT: F 105 ILE cc_start: 0.5153 (OUTLIER) cc_final: 0.4574 (tp) REVERT: F 307 TYR cc_start: 0.5232 (m-80) cc_final: 0.4995 (m-80) REVERT: F 421 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.5729 (t70) REVERT: F 483 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7338 (ptmt) REVERT: F 626 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6674 (mp10) outliers start: 63 outliers final: 35 residues processed: 233 average time/residue: 1.4942 time to fit residues: 407.8351 Evaluate side-chains 207 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 3.055 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 THR 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 201 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 626 GLN Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 194 GLN 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 F residue 25 VAL Chi-restraints excluded: chain F residue 40 LEU 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 339 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 120 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 305 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 342 optimal weight: 30.0000 chunk 262 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 HIS C 37 GLN D 109 ASN F 501 GLN F 536 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.236002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173964 restraints weight = 33131.520| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 7.03 r_work: 0.3418 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 1.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 30840 Z= 0.128 Angle : 0.622 19.285 41868 Z= 0.323 Chirality : 0.047 0.223 4740 Planarity : 0.005 0.114 5448 Dihedral : 4.373 55.904 4136 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.97 % Favored : 92.63 % Rotamer: Outliers : 1.58 % Allowed : 31.51 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3774 helix: 1.11 (0.16), residues: 1154 sheet: 0.55 (0.22), residues: 654 loop : -2.28 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.047 0.001 HIS B 536 PHE 0.019 0.001 PHE F 445 TYR 0.034 0.001 TYR B 537 ARG 0.022 0.000 ARG B 535 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 1124) hydrogen bonds : angle 4.10558 ( 3084) covalent geometry : bond 0.00285 (30840) covalent geometry : angle 0.62155 (41868) ********************** 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 225 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 3.420 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 380 ILE cc_start: -0.0012 (OUTLIER) cc_final: -0.0343 (pt) REVERT: A 429 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7156 (mm) REVERT: B 461 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7085 (mtmt) REVERT: B 464 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7224 (tp) REVERT: C 187 MET cc_start: 0.8691 (mmt) cc_final: 0.8415 (tpp) REVERT: C 509 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: C 556 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: C 560 ASP cc_start: 0.8206 (m-30) cc_final: 0.8003 (m-30) REVERT: C 590 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 604 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7913 (mm-30) REVERT: C 617 GLU cc_start: 0.8150 (tp30) cc_final: 0.7931 (tp30) REVERT: D 187 MET cc_start: 0.8672 (mmt) cc_final: 0.8433 (tpp) REVERT: D 509 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7839 (mtt) REVERT: D 626 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: E 95 LEU cc_start: 0.7387 (mp) cc_final: 0.7136 (mt) REVERT: E 306 ASP cc_start: 0.7114 (m-30) cc_final: 0.6765 (m-30) REVERT: E 365 MET cc_start: 0.3177 (mmt) cc_final: 0.1589 (mpt) REVERT: E 634 THR cc_start: 0.7903 (m) cc_final: 0.7606 (p) REVERT: F 44 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4185 (m-10) REVERT: F 105 ILE cc_start: 0.5126 (OUTLIER) cc_final: 0.4598 (tp) REVERT: F 421 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.5913 (t70) REVERT: F 483 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7400 (ptmt) outliers start: 52 outliers final: 31 residues processed: 213 average time/residue: 1.3329 time to fit residues: 341.0495 Evaluate side-chains 199 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 3.364 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 380 ILE 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 127 CYS 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 43 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 PHE 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 113 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 626 GLN Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 40 LEU 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 339 ILE Chi-restraints excluded: chain F residue 421 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 267 optimal weight: 0.0570 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 204 optimal weight: 0.9980 chunk 322 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS C 109 ASN ** D 366 HIS ** 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 = 0.4524 r_free = 0.4524 target = 0.232420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.169860 restraints weight = 32862.254| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 7.14 r_work: 0.3363 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 1.4613 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= 0.132 Angle : 0.646 17.390 41868 Z= 0.334 Chirality : 0.049 0.968 4740 Planarity : 0.005 0.112 5448 Dihedral : 4.361 55.906 4136 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.73 % Favored : 92.90 % Rotamer: Outliers : 1.86 % Allowed : 31.51 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3774 helix: 1.13 (0.16), residues: 1152 sheet: 0.50 (0.22), residues: 646 loop : -2.23 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 440 HIS 0.005 0.001 HIS B 208 PHE 0.026 0.002 PHE E 445 TYR 0.033 0.002 TYR B 281 ARG 0.036 0.001 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1124) hydrogen bonds : angle 4.07917 ( 3084) covalent geometry : bond 0.00297 (30840) covalent geometry : angle 0.64550 (41868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20514.31 seconds wall clock time: 355 minutes 16.93 seconds (21316.93 seconds total)