Starting phenix.real_space_refine on Thu Mar 5 18:46:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe4_20322/03_2026/6pe4_20322.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 156 5.16 5 C 16229 2.51 5 N 4021 2.21 5 O 4508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24914 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6142 Classifications: {'peptide': 758} Link IDs: {'PTRANS': 21, 'TRANS': 736} Chain breaks: 2 Chain: "B" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2802 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 554 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 561 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1484 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1149 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "I" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "J" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "K" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "L" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "N" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "O" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "P" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "Q" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2712 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 4.97, per 1000 atoms: 0.20 Number of scatterers: 24914 At special positions: 0 Unit cell: (150.87, 145.52, 129.47, 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 156 16.00 O 4508 8.00 N 4021 7.00 C 16229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 781.9 milliseconds 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 6 sheets defined 70.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 4.223A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 76 Processing helix chain 'A' and resid 104 through 133 removed outlier: 4.145A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.596A pdb=" N PHE A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.535A pdb=" N LEU A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.777A pdb=" N LYS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.560A pdb=" N ASN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.762A pdb=" N ASP A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.564A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.841A pdb=" N TRP A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.511A pdb=" N SER A 326 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.876A pdb=" N LEU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 410 through 423 removed outlier: 3.516A pdb=" N PHE A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.519A pdb=" N PHE A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.544A pdb=" N PHE A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.904A pdb=" N HIS A 523 " --> pdb=" O TRP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 552 removed outlier: 4.121A pdb=" N ASN A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.870A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.556A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.599A pdb=" N MET A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.503A pdb=" N TRP A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.689A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 650 through 658 removed outlier: 3.561A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 755 removed outlier: 3.558A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.645A pdb=" N GLY A 760 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 761 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 784 removed outlier: 4.078A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 803 removed outlier: 4.040A pdb=" N SER A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.715A pdb=" N ALA A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 removed outlier: 3.516A pdb=" N CYS B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.535A pdb=" N PHE D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.598A pdb=" N TYR D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.603A pdb=" N LEU D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.570A pdb=" N GLN D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 116 removed outlier: 3.817A pdb=" N LYS D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.539A pdb=" N SER D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 141 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.578A pdb=" N GLU D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.597A pdb=" N PHE D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 200 removed outlier: 3.599A pdb=" N GLU D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 226 removed outlier: 3.824A pdb=" N CYS D 207 " --> pdb=" O PRO D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.704A pdb=" N VAL D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 299 removed outlier: 3.810A pdb=" N PHE D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 331 removed outlier: 3.799A pdb=" N TRP D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 removed outlier: 3.701A pdb=" N VAL E 8 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE E 21 " --> pdb=" O MET E 17 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.063A pdb=" N ILE E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 33 removed outlier: 3.893A pdb=" N LEU F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.959A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 40 Processing helix chain 'G' and resid 41 through 45 removed outlier: 3.778A pdb=" N ILE G 45 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 removed outlier: 3.502A pdb=" N PHE G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 3.895A pdb=" N TRP G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 removed outlier: 4.259A pdb=" N LYS G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.608A pdb=" N CYS G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA G 111 " --> pdb=" O CYS G 107 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 114 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 135 through 177 Processing helix chain 'G' and resid 180 through 206 removed outlier: 4.072A pdb=" N VAL G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G 188 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE G 193 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 194 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 48 removed outlier: 3.766A pdb=" N GLY H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.672A pdb=" N LEU H 55 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 56' Processing helix chain 'H' and resid 60 through 81 removed outlier: 3.764A pdb=" N ILE H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 126 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'H' and resid 133 through 144 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.685A pdb=" N LEU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 4.147A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA I 20 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.563A pdb=" N LEU I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 50' Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.617A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.779A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 136 removed outlier: 3.851A pdb=" N PHE I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 152 removed outlier: 3.558A pdb=" N LEU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 43 removed outlier: 4.409A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER J 19 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.570A pdb=" N LEU J 49 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 46 through 50' Processing helix chain 'J' and resid 54 through 76 removed outlier: 3.520A pdb=" N ALA J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 119 removed outlier: 3.620A pdb=" N GLY J 87 " --> pdb=" O ALA J 83 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 152 removed outlier: 4.419A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU J 141 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 39 removed outlier: 4.344A pdb=" N PHE K 12 " --> pdb=" O TYR K 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY K 16 " --> pdb=" O PHE K 12 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA K 20 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.752A pdb=" N GLY K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 119 removed outlier: 3.619A pdb=" N ALA K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 121 No H-bonds generated for 'chain 'K' and resid 120 through 121' Processing helix chain 'K' and resid 122 through 123 No H-bonds generated for 'chain 'K' and resid 122 through 123' Processing helix chain 'K' and resid 124 through 153 removed outlier: 3.859A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 41 removed outlier: 4.136A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA L 20 " --> pdb=" O GLY L 16 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 75 removed outlier: 4.005A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 78 No H-bonds generated for 'chain 'L' and resid 76 through 78' Processing helix chain 'L' and resid 83 through 119 removed outlier: 3.881A pdb=" N VAL L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA L 114 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 124 No H-bonds generated for 'chain 'L' and resid 122 through 124' Processing helix chain 'L' and resid 125 through 152 removed outlier: 3.585A pdb=" N PHE L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU L 141 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 43 removed outlier: 4.047A pdb=" N PHE M 12 " --> pdb=" O TYR M 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY M 13 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE M 23 " --> pdb=" O SER M 19 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 50 removed outlier: 4.044A pdb=" N LEU M 49 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 46 through 50' Processing helix chain 'M' and resid 54 through 76 removed outlier: 4.014A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY M 67 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 76 " --> pdb=" O VAL M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 119 removed outlier: 3.748A pdb=" N SER M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 125 through 151 removed outlier: 3.899A pdb=" N PHE M 135 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN M 151 " --> pdb=" O ALA M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 154 No H-bonds generated for 'chain 'M' and resid 152 through 154' Processing helix chain 'N' and resid 9 through 43 removed outlier: 4.106A pdb=" N GLY N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE N 23 " --> pdb=" O SER N 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER N 35 " --> pdb=" O GLY N 31 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL N 37 " --> pdb=" O ALA N 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 50 removed outlier: 3.717A pdb=" N LEU N 49 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 76 removed outlier: 4.065A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY N 67 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR N 76 " --> pdb=" O VAL N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 119 removed outlier: 3.985A pdb=" N ALA N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 154 removed outlier: 4.530A pdb=" N GLY N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA N 154 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 43 removed outlier: 4.359A pdb=" N GLY O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA O 14 " --> pdb=" O PRO O 10 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE O 21 " --> pdb=" O CYS O 17 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR O 30 " --> pdb=" O LEU O 26 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY O 38 " --> pdb=" O LYS O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 50 removed outlier: 3.717A pdb=" N LEU O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 61 Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'O' and resid 83 through 119 removed outlier: 3.768A pdb=" N VAL O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 124 No H-bonds generated for 'chain 'O' and resid 122 through 124' Processing helix chain 'O' and resid 125 through 152 removed outlier: 3.655A pdb=" N PHE O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU O 141 " --> pdb=" O GLU O 137 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 removed outlier: 3.663A pdb=" N GLY P 16 " --> pdb=" O PHE P 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA P 20 " --> pdb=" O GLY P 16 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE P 21 " --> pdb=" O CYS P 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR P 30 " --> pdb=" O LEU P 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 45 No H-bonds generated for 'chain 'P' and resid 44 through 45' Processing helix chain 'P' and resid 46 through 50 removed outlier: 3.671A pdb=" N LEU P 49 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 61 through 76 removed outlier: 3.820A pdb=" N ILE P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 118 removed outlier: 3.747A pdb=" N ALA P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE P 106 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 136 removed outlier: 4.179A pdb=" N GLY P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET P 129 " --> pdb=" O LEU P 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE P 135 " --> pdb=" O LEU P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 152 removed outlier: 3.547A pdb=" N LEU P 141 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 removed outlier: 3.597A pdb=" N TYR Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 117 removed outlier: 3.609A pdb=" N GLU Q 112 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER Q 115 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Q 116 " --> pdb=" O GLU Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 134 Processing helix chain 'Q' and resid 140 through 150 removed outlier: 3.546A pdb=" N GLN Q 144 " --> pdb=" O ASP Q 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU Q 148 " --> pdb=" O GLN Q 144 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN Q 150 " --> pdb=" O SER Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 211 removed outlier: 3.687A pdb=" N ALA Q 205 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU Q 206 " --> pdb=" O ASN Q 202 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA Q 207 " --> pdb=" O GLY Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 removed outlier: 3.868A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 253 Processing helix chain 'Q' and resid 302 through 308 Processing helix chain 'Q' and resid 309 through 312 Processing helix chain 'Q' and resid 337 through 348 removed outlier: 3.908A pdb=" N ALA Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR Q 347 " --> pdb=" O ALA Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 380 Processing helix chain 'Q' and resid 407 through 421 removed outlier: 3.671A pdb=" N GLU Q 420 " --> pdb=" O LYS Q 416 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Q 421 " --> pdb=" O LEU Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 434 removed outlier: 3.806A pdb=" N LYS Q 434 " --> pdb=" O ARG Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 470 Processing helix chain 'Q' and resid 471 through 476 Processing helix chain 'Q' and resid 480 through 490 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.243A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 217 removed outlier: 3.561A pdb=" N VAL A 216 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 323 through 325 Processing sheet with id=AA5, first strand: chain 'Q' and resid 446 through 448 Processing sheet with id=AA6, first strand: chain 'Q' and resid 451 through 452 removed outlier: 3.692A pdb=" N GLY Q 455 " --> pdb=" O ALA Q 452 " (cutoff:3.500A) 1526 hydrogen bonds defined for protein. 4506 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: 3.95 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6700 1.33 - 1.46: 5103 1.46 - 1.58: 13353 1.58 - 1.70: 1 1.70 - 1.82: 246 Bond restraints: 25403 Sorted by residual: bond pdb=" N GLU H 145 " pdb=" CA GLU H 145 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 6.92e+00 bond pdb=" N GLU I 137 " pdb=" CA GLU I 137 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.28e-02 6.10e+03 6.42e+00 bond pdb=" CB VAL H 105 " pdb=" CG2 VAL H 105 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" N LYS D 163 " pdb=" CA LYS D 163 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.87e+00 bond pdb=" N ARG K 46 " pdb=" CA ARG K 46 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.51e+00 ... (remaining 25398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 33993 3.67 - 7.34: 413 7.34 - 11.00: 66 11.00 - 14.67: 9 14.67 - 18.34: 2 Bond angle restraints: 34483 Sorted by residual: angle pdb=" C PHE Q 134 " pdb=" N ASP Q 135 " pdb=" CA ASP Q 135 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" CA LEU A 649 " pdb=" CB LEU A 649 " pdb=" CG LEU A 649 " ideal model delta sigma weight residual 116.30 134.64 -18.34 3.50e+00 8.16e-02 2.75e+01 angle pdb=" C LEU Q 105 " pdb=" N THR Q 106 " pdb=" CA THR Q 106 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C LEU E 53 " pdb=" N CYS E 54 " pdb=" CA CYS E 54 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" CA LEU K 49 " pdb=" CB LEU K 49 " pdb=" CG LEU K 49 " ideal model delta sigma weight residual 116.30 133.34 -17.04 3.50e+00 8.16e-02 2.37e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 14010 15.80 - 31.60: 684 31.60 - 47.40: 156 47.40 - 63.20: 12 63.20 - 79.00: 17 Dihedral angle restraints: 14879 sinusoidal: 5517 harmonic: 9362 Sorted by residual: dihedral pdb=" CA PRO D 201 " pdb=" C PRO D 201 " pdb=" N GLU D 202 " pdb=" CA GLU D 202 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLY A 452 " pdb=" C GLY A 452 " pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ARG N 153 " pdb=" C ARG N 153 " pdb=" N ALA N 154 " pdb=" CA ALA N 154 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 14876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3190 0.066 - 0.132: 774 0.132 - 0.198: 104 0.198 - 0.265: 15 0.265 - 0.331: 3 Chirality restraints: 4086 Sorted by residual: chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA PHE D 133 " pdb=" N PHE D 133 " pdb=" C PHE D 133 " pdb=" CB PHE D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL L 55 " pdb=" CA VAL L 55 " pdb=" CG1 VAL L 55 " pdb=" CG2 VAL L 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4083 not shown) Planarity restraints: 4310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 46 " 0.596 9.50e-02 1.11e+02 2.67e-01 4.36e+01 pdb=" NE ARG K 46 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG K 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 46 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 46 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 77 " 0.023 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP G 77 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP G 77 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP G 77 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 77 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP G 77 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 77 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 77 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 647 " 0.023 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 647 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 647 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 647 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 647 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 647 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 647 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 647 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 647 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 647 " 0.004 2.00e-02 2.50e+03 ... (remaining 4307 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 805 2.71 - 3.26: 24354 3.26 - 3.81: 38547 3.81 - 4.35: 50944 4.35 - 4.90: 85741 Nonbonded interactions: 200391 Sorted by model distance: nonbonded pdb=" O MET H 65 " pdb=" OE2 GLU H 145 " model vdw 2.164 3.040 nonbonded pdb=" O TYR D 249 " pdb=" OG1 THR D 253 " model vdw 2.240 3.040 nonbonded pdb=" NE2 GLN K 122 " pdb=" O GLU Q 420 " model vdw 2.285 3.120 nonbonded pdb=" OG SER H 112 " pdb=" O SER H 144 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.307 3.040 ... (remaining 200386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and resid 2 through 159) selection = (chain 'J' and resid 2 through 159) selection = (chain 'K' and resid 2 through 159) selection = (chain 'L' and resid 2 through 159) selection = (chain 'M' and resid 2 through 159) selection = (chain 'N' and resid 2 through 159) selection = chain 'O' selection = chain 'P' } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.008 0.083 25403 Z= 0.328 Angle : 1.100 18.339 34483 Z= 0.557 Chirality : 0.058 0.331 4086 Planarity : 0.008 0.267 4310 Dihedral : 10.556 78.997 8925 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.11), residues: 3255 helix: -2.33 (0.08), residues: 2237 sheet: -1.70 (0.57), residues: 69 loop : -3.38 (0.16), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 21 TYR 0.027 0.003 TYR Q 486 PHE 0.058 0.003 PHE D 192 TRP 0.060 0.004 TRP G 77 HIS 0.012 0.002 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00804 (25403) covalent geometry : angle 1.09978 (34483) hydrogen bonds : bond 0.20105 ( 1524) hydrogen bonds : angle 6.84353 ( 4506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 447 time to evaluate : 0.942 Fit side-chains REVERT: A 82 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8096 (ttpp) REVERT: A 143 PHE cc_start: 0.8665 (t80) cc_final: 0.7937 (t80) REVERT: A 153 LEU cc_start: 0.7967 (tm) cc_final: 0.7382 (mm) REVERT: A 445 LYS cc_start: 0.7584 (tptp) cc_final: 0.6701 (tttt) REVERT: A 776 MET cc_start: 0.7221 (ttm) cc_final: 0.6941 (mtt) REVERT: D 263 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 334 GLN cc_start: 0.7482 (tp40) cc_final: 0.7221 (mt0) REVERT: F 71 PHE cc_start: 0.7675 (t80) cc_final: 0.6866 (m-80) REVERT: G 58 MET cc_start: 0.8894 (ttp) cc_final: 0.8674 (ttm) REVERT: G 102 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8230 (tt) REVERT: J 1 MET cc_start: 0.5609 (mtm) cc_final: 0.4100 (tpp) REVERT: J 155 THR cc_start: 0.8606 (p) cc_final: 0.8401 (p) REVERT: K 47 PRO cc_start: 0.9023 (Cg_endo) cc_final: 0.8821 (Cg_exo) REVERT: K 106 PHE cc_start: 0.8021 (m-10) cc_final: 0.7746 (t80) REVERT: L 1 MET cc_start: 0.6667 (ttp) cc_final: 0.6309 (ttp) REVERT: L 34 LYS cc_start: 0.9349 (tptt) cc_final: 0.9110 (tptp) REVERT: N 96 SER cc_start: 0.9018 (t) cc_final: 0.8691 (m) REVERT: P 135 PHE cc_start: 0.8701 (m-10) cc_final: 0.8425 (m-80) REVERT: Q 227 MET cc_start: 0.9085 (mmt) cc_final: 0.8882 (mmm) REVERT: Q 250 LEU cc_start: 0.8124 (tm) cc_final: 0.7924 (tp) REVERT: Q 364 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6778 (tt0) outliers start: 8 outliers final: 4 residues processed: 454 average time/residue: 0.1781 time to fit residues: 123.2201 Evaluate side-chains 312 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 307 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 311 GLN A 384 ASN A 563 ASN A 614 ASN A 714 HIS D 7 ASN D 78 HIS D 125 GLN D 302 GLN E 30 GLN E 55 GLN F 72 GLN I 121 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN Q 326 ASN Q 366 GLN Q 469 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091856 restraints weight = 30048.197| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.52 r_work: 0.2861 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25403 Z= 0.128 Angle : 0.599 11.862 34483 Z= 0.307 Chirality : 0.040 0.203 4086 Planarity : 0.005 0.047 4310 Dihedral : 5.166 51.755 3525 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 1.67 % Allowed : 7.21 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3255 helix: -0.26 (0.10), residues: 2261 sheet: -0.75 (0.63), residues: 58 loop : -2.98 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 194 TYR 0.016 0.001 TYR H 90 PHE 0.033 0.001 PHE D 133 TRP 0.024 0.001 TRP A 647 HIS 0.007 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00254 (25403) covalent geometry : angle 0.59850 (34483) hydrogen bonds : bond 0.05620 ( 1524) hydrogen bonds : angle 4.05580 ( 4506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.925 Fit side-chains REVERT: A 82 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8194 (ttpp) REVERT: A 143 PHE cc_start: 0.8701 (t80) cc_final: 0.8037 (t80) REVERT: A 445 LYS cc_start: 0.7683 (tptp) cc_final: 0.6832 (tttt) REVERT: A 530 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8946 (tp) REVERT: A 537 MET cc_start: 0.9107 (mtm) cc_final: 0.8858 (mtm) REVERT: A 776 MET cc_start: 0.8354 (ttm) cc_final: 0.7774 (mtt) REVERT: D 153 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8563 (mt) REVERT: D 263 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7785 (tp30) REVERT: D 334 GLN cc_start: 0.7880 (tp40) cc_final: 0.7512 (mm-40) REVERT: G 53 ARG cc_start: 0.8873 (mmm160) cc_final: 0.8610 (mtp85) REVERT: G 58 MET cc_start: 0.9057 (ttp) cc_final: 0.8835 (ttm) REVERT: H 9 ILE cc_start: 0.8979 (tt) cc_final: 0.8609 (mm) REVERT: H 97 MET cc_start: 0.9137 (mmp) cc_final: 0.8699 (mmp) REVERT: H 145 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: J 1 MET cc_start: 0.6259 (mtm) cc_final: 0.4560 (tpp) REVERT: K 106 PHE cc_start: 0.8264 (m-10) cc_final: 0.7776 (t80) REVERT: K 119 SER cc_start: 0.9009 (t) cc_final: 0.8554 (m) REVERT: K 137 GLU cc_start: 0.8825 (tp30) cc_final: 0.8613 (mm-30) REVERT: L 1 MET cc_start: 0.6981 (ttp) cc_final: 0.6770 (ttp) REVERT: N 106 PHE cc_start: 0.8280 (m-10) cc_final: 0.7750 (t80) REVERT: Q 111 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7845 (mp) REVERT: Q 129 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7705 (tp-100) REVERT: Q 324 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7650 (mp) outliers start: 44 outliers final: 14 residues processed: 402 average time/residue: 0.1570 time to fit residues: 100.4441 Evaluate side-chains 322 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 282 optimal weight: 50.0000 chunk 96 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 284 optimal weight: 0.0270 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN D 7 ASN D 125 GLN G 100 ASN I 82 GLN O 121 GLN Q 326 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.082288 restraints weight = 30350.108| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.53 r_work: 0.2630 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25403 Z= 0.209 Angle : 0.662 12.388 34483 Z= 0.333 Chirality : 0.043 0.236 4086 Planarity : 0.004 0.042 4310 Dihedral : 5.034 54.806 3519 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.88 % Allowed : 9.11 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3255 helix: 0.51 (0.11), residues: 2252 sheet: -0.23 (0.66), residues: 56 loop : -2.72 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 762 TYR 0.023 0.002 TYR H 90 PHE 0.036 0.002 PHE D 133 TRP 0.025 0.002 TRP A 647 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00512 (25403) covalent geometry : angle 0.66216 (34483) hydrogen bonds : bond 0.06337 ( 1524) hydrogen bonds : angle 3.91126 ( 4506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 316 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8089 (ptmt) REVERT: A 143 PHE cc_start: 0.8614 (t80) cc_final: 0.7841 (t80) REVERT: A 279 LYS cc_start: 0.7464 (pttm) cc_final: 0.7238 (ptmt) REVERT: A 445 LYS cc_start: 0.7721 (tptp) cc_final: 0.6755 (tttt) REVERT: A 530 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8993 (tp) REVERT: A 556 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8871 (tp) REVERT: A 826 ASP cc_start: 0.8706 (t0) cc_final: 0.8468 (t0) REVERT: D 153 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8756 (mt) REVERT: D 154 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (m) REVERT: D 263 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7788 (mm-30) REVERT: D 334 GLN cc_start: 0.7999 (tp40) cc_final: 0.7602 (mm-40) REVERT: F 56 TYR cc_start: 0.7621 (t80) cc_final: 0.7150 (t80) REVERT: F 71 PHE cc_start: 0.7500 (t80) cc_final: 0.6600 (m-80) REVERT: H 9 ILE cc_start: 0.8984 (tt) cc_final: 0.8634 (mm) REVERT: H 145 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: J 1 MET cc_start: 0.6077 (mtm) cc_final: 0.4226 (tpp) REVERT: K 106 PHE cc_start: 0.8261 (m-10) cc_final: 0.7600 (t80) REVERT: K 119 SER cc_start: 0.9047 (t) cc_final: 0.8601 (m) REVERT: K 131 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9132 (tp) REVERT: K 144 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8911 (tp) REVERT: L 3 GLU cc_start: 0.8705 (tt0) cc_final: 0.8378 (tt0) REVERT: N 42 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8953 (t) REVERT: N 106 PHE cc_start: 0.8298 (m-10) cc_final: 0.7527 (t80) REVERT: Q 129 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7782 (tp-100) REVERT: Q 131 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8126 (tttm) REVERT: Q 324 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7322 (mp) outliers start: 76 outliers final: 43 residues processed: 373 average time/residue: 0.1618 time to fit residues: 95.7097 Evaluate side-chains 358 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 178 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 384 ASN D 125 GLN D 255 HIS Q 128 GLN Q 307 GLN Q 326 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.082684 restraints weight = 30102.223| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.49 r_work: 0.2599 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 25403 Z= 0.282 Angle : 0.714 12.252 34483 Z= 0.359 Chirality : 0.046 0.252 4086 Planarity : 0.005 0.050 4310 Dihedral : 5.184 59.357 3519 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 3.61 % Allowed : 10.47 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3255 helix: 0.62 (0.11), residues: 2260 sheet: -0.24 (0.69), residues: 56 loop : -2.68 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 799 TYR 0.026 0.002 TYR H 90 PHE 0.038 0.002 PHE D 133 TRP 0.020 0.002 TRP A 647 HIS 0.007 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00698 (25403) covalent geometry : angle 0.71407 (34483) hydrogen bonds : bond 0.06949 ( 1524) hydrogen bonds : angle 3.98825 ( 4506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 307 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8114 (ptmt) REVERT: A 136 ASN cc_start: 0.8048 (m-40) cc_final: 0.7803 (m110) REVERT: A 143 PHE cc_start: 0.8682 (t80) cc_final: 0.7626 (t80) REVERT: A 279 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7231 (ptmt) REVERT: A 445 LYS cc_start: 0.7749 (tptp) cc_final: 0.6759 (tttt) REVERT: A 826 ASP cc_start: 0.8792 (t0) cc_final: 0.8512 (t0) REVERT: D 39 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8744 (mt) REVERT: D 148 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8487 (mp) REVERT: D 153 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8902 (mt) REVERT: D 263 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7846 (mm-30) REVERT: D 334 GLN cc_start: 0.8084 (tp40) cc_final: 0.7726 (mm-40) REVERT: F 71 PHE cc_start: 0.7526 (t80) cc_final: 0.6632 (m-80) REVERT: G 95 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7305 (ptt90) REVERT: H 9 ILE cc_start: 0.9017 (tt) cc_final: 0.8684 (mm) REVERT: H 145 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: I 3 GLU cc_start: 0.8875 (tp30) cc_final: 0.8656 (tp30) REVERT: J 1 MET cc_start: 0.6198 (mtm) cc_final: 0.4141 (tpp) REVERT: K 106 PHE cc_start: 0.8366 (m-10) cc_final: 0.7712 (t80) REVERT: L 3 GLU cc_start: 0.8801 (tt0) cc_final: 0.8459 (tt0) REVERT: N 42 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8968 (t) REVERT: N 106 PHE cc_start: 0.8241 (m-10) cc_final: 0.7531 (t80) REVERT: N 131 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (mt) REVERT: P 68 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8985 (tp) REVERT: Q 92 TYR cc_start: 0.7724 (t80) cc_final: 0.7498 (t80) REVERT: Q 111 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7638 (mp) REVERT: Q 129 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7843 (tp-100) REVERT: Q 131 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8130 (tttm) REVERT: Q 324 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7350 (mp) REVERT: Q 360 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7753 (mm-40) outliers start: 95 outliers final: 61 residues processed: 380 average time/residue: 0.1526 time to fit residues: 92.6736 Evaluate side-chains 368 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 295 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 222 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 756 GLN D 125 GLN Q 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.084530 restraints weight = 30023.796| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.41 r_work: 0.2733 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25403 Z= 0.185 Angle : 0.612 11.176 34483 Z= 0.311 Chirality : 0.042 0.222 4086 Planarity : 0.004 0.047 4310 Dihedral : 4.931 57.512 3519 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 3.64 % Allowed : 11.46 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3255 helix: 0.99 (0.11), residues: 2249 sheet: -0.26 (0.70), residues: 54 loop : -2.51 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.023 0.001 TYR H 90 PHE 0.036 0.001 PHE D 133 TRP 0.015 0.001 TRP A 647 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00444 (25403) covalent geometry : angle 0.61218 (34483) hydrogen bonds : bond 0.05938 ( 1524) hydrogen bonds : angle 3.79175 ( 4506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 323 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8196 (ptmt) REVERT: A 136 ASN cc_start: 0.8177 (m-40) cc_final: 0.7956 (m110) REVERT: A 143 PHE cc_start: 0.8684 (t80) cc_final: 0.7676 (t80) REVERT: A 279 LYS cc_start: 0.7511 (pttm) cc_final: 0.7277 (ptmt) REVERT: A 445 LYS cc_start: 0.7853 (tptp) cc_final: 0.6901 (tttm) REVERT: A 530 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9067 (tp) REVERT: A 537 MET cc_start: 0.9147 (mtm) cc_final: 0.8901 (mtm) REVERT: A 556 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9027 (tp) REVERT: A 761 PHE cc_start: 0.8182 (m-10) cc_final: 0.7963 (m-80) REVERT: A 826 ASP cc_start: 0.8768 (t0) cc_final: 0.8415 (t0) REVERT: D 148 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8676 (mp) REVERT: D 153 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8654 (mt) REVERT: D 263 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 334 GLN cc_start: 0.8072 (tp40) cc_final: 0.7744 (mm-40) REVERT: F 71 PHE cc_start: 0.7599 (t80) cc_final: 0.6723 (m-80) REVERT: G 95 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7300 (ptt90) REVERT: H 9 ILE cc_start: 0.9004 (tt) cc_final: 0.8672 (mm) REVERT: H 145 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: I 3 GLU cc_start: 0.8873 (tp30) cc_final: 0.8612 (tp30) REVERT: J 1 MET cc_start: 0.6401 (mtm) cc_final: 0.4429 (tpp) REVERT: K 106 PHE cc_start: 0.8413 (m-10) cc_final: 0.7937 (t80) REVERT: K 133 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8796 (mp) REVERT: K 144 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8973 (tp) REVERT: L 3 GLU cc_start: 0.8824 (tt0) cc_final: 0.8480 (tt0) REVERT: L 106 PHE cc_start: 0.8791 (m-10) cc_final: 0.8537 (m-80) REVERT: N 42 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.9005 (t) REVERT: N 106 PHE cc_start: 0.8286 (m-10) cc_final: 0.7760 (t80) REVERT: O 139 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8775 (mp) REVERT: Q 92 TYR cc_start: 0.7766 (t80) cc_final: 0.7477 (t80) REVERT: Q 111 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7633 (mp) REVERT: Q 131 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8185 (tttm) REVERT: Q 324 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7441 (mp) REVERT: Q 360 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7746 (mm-40) outliers start: 96 outliers final: 53 residues processed: 398 average time/residue: 0.1615 time to fit residues: 102.2819 Evaluate side-chains 381 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 315 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN O 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.085233 restraints weight = 29859.305| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.44 r_work: 0.2613 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25403 Z= 0.214 Angle : 0.636 13.064 34483 Z= 0.321 Chirality : 0.043 0.236 4086 Planarity : 0.004 0.048 4310 Dihedral : 4.901 52.908 3519 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 3.83 % Allowed : 11.80 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3255 helix: 1.05 (0.11), residues: 2249 sheet: -0.18 (0.68), residues: 56 loop : -2.43 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.023 0.001 TYR H 90 PHE 0.037 0.002 PHE D 133 TRP 0.014 0.001 TRP A 647 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00525 (25403) covalent geometry : angle 0.63616 (34483) hydrogen bonds : bond 0.06215 ( 1524) hydrogen bonds : angle 3.80964 ( 4506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 309 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8156 (ptmt) REVERT: A 136 ASN cc_start: 0.7992 (m-40) cc_final: 0.7742 (m110) REVERT: A 143 PHE cc_start: 0.8591 (t80) cc_final: 0.7476 (t80) REVERT: A 445 LYS cc_start: 0.7699 (tptp) cc_final: 0.6728 (tttm) REVERT: A 761 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: A 826 ASP cc_start: 0.8713 (t0) cc_final: 0.8322 (t0) REVERT: D 148 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8398 (mp) REVERT: D 153 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 263 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7806 (mm-30) REVERT: D 334 GLN cc_start: 0.8039 (tp40) cc_final: 0.7674 (mm-40) REVERT: F 71 PHE cc_start: 0.7437 (t80) cc_final: 0.6564 (m-80) REVERT: G 95 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7303 (ptt90) REVERT: G 213 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: H 9 ILE cc_start: 0.8954 (tt) cc_final: 0.8632 (mm) REVERT: H 145 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: I 3 GLU cc_start: 0.8831 (tp30) cc_final: 0.8569 (tp30) REVERT: I 68 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8791 (tp) REVERT: J 1 MET cc_start: 0.6257 (mtm) cc_final: 0.4176 (tpp) REVERT: K 106 PHE cc_start: 0.8343 (m-10) cc_final: 0.7643 (t80) REVERT: K 133 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8615 (mp) REVERT: K 144 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8901 (tp) REVERT: L 3 GLU cc_start: 0.8799 (tt0) cc_final: 0.8547 (tt0) REVERT: L 106 PHE cc_start: 0.8671 (m-10) cc_final: 0.8422 (m-80) REVERT: N 106 PHE cc_start: 0.8181 (m-10) cc_final: 0.7444 (t80) REVERT: O 139 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8635 (mp) REVERT: Q 92 TYR cc_start: 0.7678 (t80) cc_final: 0.7386 (t80) REVERT: Q 111 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7533 (mp) REVERT: Q 324 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7363 (mp) REVERT: Q 360 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7732 (mm-40) outliers start: 101 outliers final: 65 residues processed: 383 average time/residue: 0.1612 time to fit residues: 97.3715 Evaluate side-chains 376 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 327 VAL Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.082830 restraints weight = 30093.599| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.40 r_work: 0.2655 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25403 Z= 0.164 Angle : 0.593 14.478 34483 Z= 0.298 Chirality : 0.041 0.213 4086 Planarity : 0.004 0.045 4310 Dihedral : 4.730 55.398 3519 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 3.49 % Allowed : 12.52 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3255 helix: 1.28 (0.11), residues: 2254 sheet: -0.23 (0.70), residues: 54 loop : -2.37 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 762 TYR 0.021 0.001 TYR H 90 PHE 0.036 0.001 PHE D 133 TRP 0.012 0.001 TRP A 647 HIS 0.005 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00389 (25403) covalent geometry : angle 0.59265 (34483) hydrogen bonds : bond 0.05563 ( 1524) hydrogen bonds : angle 3.67958 ( 4506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 318 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8143 (ptmt) REVERT: A 136 ASN cc_start: 0.8026 (m-40) cc_final: 0.7792 (m110) REVERT: A 143 PHE cc_start: 0.8610 (t80) cc_final: 0.7498 (t80) REVERT: A 279 LYS cc_start: 0.7479 (pttm) cc_final: 0.7214 (ptmt) REVERT: A 445 LYS cc_start: 0.7725 (tptp) cc_final: 0.6778 (tttm) REVERT: A 530 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9084 (tp) REVERT: A 556 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8876 (tp) REVERT: A 761 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: A 826 ASP cc_start: 0.8711 (t0) cc_final: 0.8321 (t0) REVERT: D 148 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (mp) REVERT: D 153 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8569 (mt) REVERT: D 263 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7876 (mm-30) REVERT: D 334 GLN cc_start: 0.7994 (tp40) cc_final: 0.7645 (mm-40) REVERT: F 71 PHE cc_start: 0.7458 (t80) cc_final: 0.6599 (m-80) REVERT: G 95 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7283 (ptt90) REVERT: G 213 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: H 9 ILE cc_start: 0.8949 (tt) cc_final: 0.8631 (mm) REVERT: H 145 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: I 3 GLU cc_start: 0.8832 (tp30) cc_final: 0.8601 (tp30) REVERT: I 68 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8828 (tp) REVERT: J 1 MET cc_start: 0.6276 (mtm) cc_final: 0.4206 (tpp) REVERT: K 106 PHE cc_start: 0.8370 (m-10) cc_final: 0.7734 (t80) REVERT: K 119 SER cc_start: 0.8988 (t) cc_final: 0.8528 (m) REVERT: K 144 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8924 (tp) REVERT: L 3 GLU cc_start: 0.8792 (tt0) cc_final: 0.8536 (tt0) REVERT: L 106 PHE cc_start: 0.8697 (m-10) cc_final: 0.8448 (m-80) REVERT: N 106 PHE cc_start: 0.8245 (m-10) cc_final: 0.7543 (t80) REVERT: Q 92 TYR cc_start: 0.7595 (t80) cc_final: 0.7232 (t80) REVERT: Q 111 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7595 (mp) REVERT: Q 324 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7432 (mp) REVERT: Q 360 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7619 (mm-40) outliers start: 92 outliers final: 58 residues processed: 383 average time/residue: 0.1614 time to fit residues: 98.2938 Evaluate side-chains 382 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 324 ILE Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Chi-restraints excluded: chain Q residue 440 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 151 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 299 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.079123 restraints weight = 30411.520| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.51 r_work: 0.2559 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25403 Z= 0.292 Angle : 0.715 13.276 34483 Z= 0.358 Chirality : 0.046 0.268 4086 Planarity : 0.005 0.053 4310 Dihedral : 5.017 56.252 3519 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 3.61 % Allowed : 12.45 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3255 helix: 0.98 (0.11), residues: 2264 sheet: -0.16 (0.69), residues: 56 loop : -2.42 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 762 TYR 0.025 0.002 TYR H 90 PHE 0.038 0.002 PHE D 133 TRP 0.014 0.002 TRP A 647 HIS 0.007 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00727 (25403) covalent geometry : angle 0.71456 (34483) hydrogen bonds : bond 0.06993 ( 1524) hydrogen bonds : angle 3.93051 ( 4506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 290 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8124 (ptmt) REVERT: A 136 ASN cc_start: 0.8101 (m-40) cc_final: 0.7860 (m110) REVERT: A 143 PHE cc_start: 0.8641 (t80) cc_final: 0.8411 (t80) REVERT: A 279 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7127 (ptmt) REVERT: A 445 LYS cc_start: 0.7768 (tptp) cc_final: 0.6766 (tttm) REVERT: A 761 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: A 769 MET cc_start: 0.7938 (tpt) cc_final: 0.7524 (mmm) REVERT: A 826 ASP cc_start: 0.8795 (t0) cc_final: 0.8432 (t0) REVERT: B 213 ASP cc_start: 0.7102 (t70) cc_final: 0.6771 (t70) REVERT: D 148 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 263 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7878 (mm-30) REVERT: D 334 GLN cc_start: 0.8091 (tp40) cc_final: 0.7525 (mt0) REVERT: F 71 PHE cc_start: 0.7445 (t80) cc_final: 0.6598 (m-80) REVERT: G 95 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7302 (ptt90) REVERT: G 213 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: H 9 ILE cc_start: 0.8990 (tt) cc_final: 0.8678 (mm) REVERT: H 145 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: I 3 GLU cc_start: 0.8889 (tp30) cc_final: 0.8632 (tp30) REVERT: I 68 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8794 (tp) REVERT: J 1 MET cc_start: 0.6358 (mtm) cc_final: 0.4192 (tpp) REVERT: K 106 PHE cc_start: 0.8389 (m-10) cc_final: 0.7705 (t80) REVERT: K 133 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8766 (mp) REVERT: L 3 GLU cc_start: 0.8820 (tt0) cc_final: 0.8559 (tt0) REVERT: L 106 PHE cc_start: 0.8744 (m-10) cc_final: 0.8488 (m-80) REVERT: N 106 PHE cc_start: 0.8281 (m-10) cc_final: 0.7545 (t80) REVERT: O 139 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8711 (mp) REVERT: Q 92 TYR cc_start: 0.7572 (t80) cc_final: 0.7247 (t80) REVERT: Q 111 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7599 (mp) REVERT: Q 360 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7761 (mm-40) outliers start: 95 outliers final: 69 residues processed: 360 average time/residue: 0.1625 time to fit residues: 92.7864 Evaluate side-chains 366 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 80 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 218 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.089488 restraints weight = 29565.233| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.50 r_work: 0.2805 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25403 Z= 0.113 Angle : 0.540 13.070 34483 Z= 0.274 Chirality : 0.039 0.170 4086 Planarity : 0.004 0.045 4310 Dihedral : 4.492 59.424 3519 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 2.39 % Allowed : 13.59 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3255 helix: 1.57 (0.11), residues: 2257 sheet: -0.39 (0.69), residues: 54 loop : -2.24 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.017 0.001 TYR H 90 PHE 0.037 0.001 PHE D 133 TRP 0.010 0.001 TRP A 647 HIS 0.003 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00226 (25403) covalent geometry : angle 0.53992 (34483) hydrogen bonds : bond 0.04503 ( 1524) hydrogen bonds : angle 3.50202 ( 4506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 327 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8174 (ptmt) REVERT: A 124 MET cc_start: 0.8524 (mtp) cc_final: 0.8270 (mtt) REVERT: A 143 PHE cc_start: 0.8645 (t80) cc_final: 0.7605 (t80) REVERT: A 216 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8475 (t) REVERT: A 445 LYS cc_start: 0.7830 (tptp) cc_final: 0.6894 (tttm) REVERT: A 556 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9020 (tp) REVERT: A 769 MET cc_start: 0.7956 (tpt) cc_final: 0.7544 (mmm) REVERT: A 826 ASP cc_start: 0.8742 (t0) cc_final: 0.8430 (t0) REVERT: D 263 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7943 (mm-30) REVERT: D 334 GLN cc_start: 0.7963 (tp40) cc_final: 0.7640 (mm-40) REVERT: F 71 PHE cc_start: 0.7488 (t80) cc_final: 0.6679 (m-80) REVERT: G 129 THR cc_start: 0.8804 (m) cc_final: 0.8462 (p) REVERT: G 211 GLU cc_start: 0.8608 (pt0) cc_final: 0.8186 (pt0) REVERT: G 213 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6873 (pm20) REVERT: H 9 ILE cc_start: 0.8979 (tt) cc_final: 0.8678 (mm) REVERT: H 145 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: I 3 GLU cc_start: 0.8805 (tp30) cc_final: 0.8569 (tp30) REVERT: J 1 MET cc_start: 0.6561 (mtm) cc_final: 0.4458 (tpp) REVERT: J 24 THR cc_start: 0.8965 (p) cc_final: 0.8685 (p) REVERT: J 42 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8753 (m) REVERT: K 106 PHE cc_start: 0.8322 (m-10) cc_final: 0.7909 (t80) REVERT: K 119 SER cc_start: 0.9013 (t) cc_final: 0.8577 (m) REVERT: K 133 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8413 (mp) REVERT: K 144 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8968 (tp) REVERT: L 3 GLU cc_start: 0.8804 (tt0) cc_final: 0.8561 (tt0) REVERT: L 50 LEU cc_start: 0.9183 (tp) cc_final: 0.8971 (tt) REVERT: L 106 PHE cc_start: 0.8781 (m-10) cc_final: 0.8574 (m-80) REVERT: M 50 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9082 (tp) REVERT: N 106 PHE cc_start: 0.8253 (m-10) cc_final: 0.7715 (t80) REVERT: Q 92 TYR cc_start: 0.7588 (t80) cc_final: 0.7304 (t80) REVERT: Q 322 LEU cc_start: 0.8396 (mp) cc_final: 0.8167 (pp) REVERT: Q 356 MET cc_start: 0.6077 (tpp) cc_final: 0.5737 (tpp) REVERT: Q 360 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (mm-40) REVERT: Q 399 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6402 (t0) outliers start: 63 outliers final: 36 residues processed: 377 average time/residue: 0.1626 time to fit residues: 97.3400 Evaluate side-chains 354 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 177 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.083062 restraints weight = 30052.429| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.50 r_work: 0.2604 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25403 Z= 0.215 Angle : 0.636 12.700 34483 Z= 0.320 Chirality : 0.043 0.243 4086 Planarity : 0.004 0.045 4310 Dihedral : 4.632 57.567 3517 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 2.16 % Allowed : 13.89 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3255 helix: 1.41 (0.11), residues: 2255 sheet: -0.22 (0.68), residues: 56 loop : -2.23 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 762 TYR 0.021 0.001 TYR H 90 PHE 0.037 0.002 PHE D 133 TRP 0.011 0.001 TRP A 647 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00532 (25403) covalent geometry : angle 0.63646 (34483) hydrogen bonds : bond 0.06061 ( 1524) hydrogen bonds : angle 3.71080 ( 4506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8129 (ptmt) REVERT: A 124 MET cc_start: 0.8385 (mtp) cc_final: 0.8155 (mtt) REVERT: A 143 PHE cc_start: 0.8596 (t80) cc_final: 0.7557 (t80) REVERT: A 445 LYS cc_start: 0.7721 (tptp) cc_final: 0.6735 (tttm) REVERT: A 754 THR cc_start: 0.8835 (t) cc_final: 0.8496 (p) REVERT: A 769 MET cc_start: 0.7802 (tpt) cc_final: 0.7444 (mmm) REVERT: A 826 ASP cc_start: 0.8837 (t0) cc_final: 0.8492 (t0) REVERT: D 110 MET cc_start: 0.9139 (tpp) cc_final: 0.8939 (mmt) REVERT: D 263 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 334 GLN cc_start: 0.8035 (tp40) cc_final: 0.7686 (mm-40) REVERT: F 71 PHE cc_start: 0.7422 (t80) cc_final: 0.6613 (m-80) REVERT: G 95 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7315 (ptt90) REVERT: G 213 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: H 9 ILE cc_start: 0.8953 (tt) cc_final: 0.8637 (mm) REVERT: H 145 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: I 3 GLU cc_start: 0.8831 (tp30) cc_final: 0.8590 (tp30) REVERT: J 1 MET cc_start: 0.6320 (mtm) cc_final: 0.4196 (tpp) REVERT: K 106 PHE cc_start: 0.8394 (m-10) cc_final: 0.7698 (t80) REVERT: K 133 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8560 (mp) REVERT: K 144 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8894 (tp) REVERT: L 3 GLU cc_start: 0.8795 (tt0) cc_final: 0.8520 (tt0) REVERT: L 106 PHE cc_start: 0.8709 (m-10) cc_final: 0.8456 (m-80) REVERT: N 106 PHE cc_start: 0.8302 (m-10) cc_final: 0.7551 (t80) REVERT: Q 92 TYR cc_start: 0.7585 (t80) cc_final: 0.7240 (t80) REVERT: Q 322 LEU cc_start: 0.8463 (mp) cc_final: 0.7850 (tt) REVERT: Q 360 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7592 (mm-40) outliers start: 57 outliers final: 45 residues processed: 349 average time/residue: 0.1629 time to fit residues: 90.6377 Evaluate side-chains 348 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 326 ASN Chi-restraints excluded: chain Q residue 360 GLN Chi-restraints excluded: chain Q residue 399 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 312 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 313 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.085376 restraints weight = 29685.617| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.46 r_work: 0.2623 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 25403 Z= 0.187 Angle : 0.755 59.180 34483 Z= 0.409 Chirality : 0.043 0.880 4086 Planarity : 0.004 0.070 4310 Dihedral : 4.555 57.619 3515 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 2.28 % Allowed : 13.89 % Favored : 83.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3255 helix: 1.43 (0.11), residues: 2254 sheet: -0.21 (0.68), residues: 56 loop : -2.24 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.021 0.001 TYR H 90 PHE 0.037 0.001 PHE D 133 TRP 0.011 0.001 TRP E 48 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00434 (25403) covalent geometry : angle 0.75544 (34483) hydrogen bonds : bond 0.05804 ( 1524) hydrogen bonds : angle 3.71189 ( 4506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5922.55 seconds wall clock time: 101 minutes 52.94 seconds (6112.94 seconds total)