Starting phenix.real_space_refine on Thu Mar 5 08:59:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.map" model { file = "/net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7u_0645/03_2026/6o7u_0645.cif" } 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= 0.003 sd= 0.366 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 136 5.16 5 C 13966 2.51 5 N 3411 2.21 5 O 3755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s 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: 21268 Number of models: 1 Model: "" Number of chains: 15 Chain: "a" Number of atoms: 5665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5665 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 17, 'TRANS': 695} Chain breaks: 4 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 7, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "b" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 330 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1466 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 2, 'TRANS': 194} Chain: "d" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2720 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 333} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "e" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 463 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "g" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1094 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "h" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "i" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "j" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1116 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" 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: "l" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "m" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "n" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "o" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1133 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Time building chain proxies: 4.82, per 1000 atoms: 0.23 Number of scatterers: 21268 At special positions: 0 Unit cell: (118.72, 115.54, 132.5, 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 136 16.00 O 3755 8.00 N 3411 7.00 C 13966 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: 1.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5102 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 4 sheets defined 76.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'a' and resid 24 through 36 Processing helix chain 'a' and resid 57 through 78 removed outlier: 4.006A pdb=" N PHE a 61 " --> pdb=" O GLN a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 118 Processing helix chain 'a' and resid 118 through 164 removed outlier: 3.743A pdb=" N GLU a 122 " --> pdb=" O ASP a 118 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS a 126 " --> pdb=" O GLU a 122 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG a 129 " --> pdb=" O ASP a 125 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU a 140 " --> pdb=" O SER a 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS a 143 " --> pdb=" O SER a 139 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN a 152 " --> pdb=" O LEU a 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL a 153 " --> pdb=" O GLU a 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE a 154 " --> pdb=" O GLN a 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS a 157 " --> pdb=" O VAL a 153 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS a 159 " --> pdb=" O PHE a 155 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE a 160 " --> pdb=" O GLU a 156 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 161 " --> pdb=" O CYS a 157 " (cutoff:3.500A) Processing helix chain 'a' and resid 248 through 260 Processing helix chain 'a' and resid 296 through 305 removed outlier: 3.707A pdb=" N LYS a 301 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 320 through 352 removed outlier: 3.588A pdb=" N THR a 324 " --> pdb=" O GLU a 320 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN a 328 " --> pdb=" O THR a 324 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP a 330 " --> pdb=" O ASN a 326 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE a 335 " --> pdb=" O ASP a 331 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 341 " --> pdb=" O ASP a 337 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU a 348 " --> pdb=" O HIS a 344 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL a 349 " --> pdb=" O THR a 345 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE a 350 " --> pdb=" O GLU a 346 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP a 352 " --> pdb=" O LEU a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 353 through 372 removed outlier: 3.756A pdb=" N ALA a 359 " --> pdb=" O PRO a 355 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR a 361 " --> pdb=" O TRP a 357 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG a 363 " --> pdb=" O ALA a 359 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR a 366 " --> pdb=" O LYS a 362 " (cutoff:3.500A) Processing helix chain 'a' and resid 388 through 390 No H-bonds generated for 'chain 'a' and resid 388 through 390' Processing helix chain 'a' and resid 391 through 406 removed outlier: 4.064A pdb=" N LYS a 400 " --> pdb=" O GLN a 396 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP a 401 " --> pdb=" O ASP a 397 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU a 404 " --> pdb=" O LYS a 400 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU a 406 " --> pdb=" O TYR a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 444 removed outlier: 4.118A pdb=" N TYR a 443 " --> pdb=" O ILE a 439 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY a 444 " --> pdb=" O VAL a 440 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 469 Proline residue: a 462 - end of helix removed outlier: 3.653A pdb=" N MET a 468 " --> pdb=" O MET a 464 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 488 removed outlier: 4.030A pdb=" N LEU a 485 " --> pdb=" O MET a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 488 through 494 removed outlier: 3.939A pdb=" N ALA a 494 " --> pdb=" O ARG a 490 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 507 Processing helix chain 'a' and resid 507 through 525 removed outlier: 3.643A pdb=" N LEU a 512 " --> pdb=" O ARG a 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU a 513 " --> pdb=" O TYR a 509 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER a 518 " --> pdb=" O MET a 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR a 520 " --> pdb=" O ALA a 516 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 569 removed outlier: 3.747A pdb=" N TRP a 568 " --> pdb=" O ASP a 565 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS a 569 " --> pdb=" O PHE a 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 565 through 569' Processing helix chain 'a' and resid 573 through 598 removed outlier: 3.566A pdb=" N PHE a 577 " --> pdb=" O ASN a 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 608 removed outlier: 3.819A pdb=" N TYR a 602 " --> pdb=" O PHE a 598 " (cutoff:3.500A) Processing helix chain 'a' and resid 610 through 626 removed outlier: 5.111A pdb=" N ILE a 619 " --> pdb=" O ILE a 615 " (cutoff:3.500A) Proline residue: a 620 - end of helix removed outlier: 3.555A pdb=" N PHE a 624 " --> pdb=" O PRO a 620 " (cutoff:3.500A) Processing helix chain 'a' and resid 628 through 642 removed outlier: 3.579A pdb=" N VAL a 637 " --> pdb=" O SER a 633 " (cutoff:3.500A) Processing helix chain 'a' and resid 654 through 664 removed outlier: 3.935A pdb=" N PHE a 662 " --> pdb=" O LEU a 658 " (cutoff:3.500A) Processing helix chain 'a' and resid 675 through 689 removed outlier: 4.078A pdb=" N VAL a 681 " --> pdb=" O ALA a 677 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL a 682 " --> pdb=" O LYS a 678 " (cutoff:3.500A) Processing helix chain 'a' and resid 689 through 703 removed outlier: 3.656A pdb=" N LEU a 695 " --> pdb=" O VAL a 691 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS a 698 " --> pdb=" O LEU a 694 " (cutoff:3.500A) Proline residue: a 699 - end of helix Processing helix chain 'a' and resid 704 through 707 removed outlier: 3.538A pdb=" N LYS a 707 " --> pdb=" O ARG a 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 704 through 707' Processing helix chain 'a' and resid 767 through 791 removed outlier: 4.056A pdb=" N HIS a 774 " --> pdb=" O ASP a 770 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE a 787 " --> pdb=" O CYS a 783 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR a 790 " --> pdb=" O CYS a 786 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA a 791 " --> pdb=" O ILE a 787 " (cutoff:3.500A) Processing helix chain 'a' and resid 794 through 815 removed outlier: 3.776A pdb=" N SER a 800 " --> pdb=" O LEU a 796 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP a 811 " --> pdb=" O SER a 807 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET a 813 " --> pdb=" O VAL a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 847 removed outlier: 3.882A pdb=" N VAL a 833 " --> pdb=" O ALA a 829 " (cutoff:3.500A) Processing helix chain 'a' and resid 852 through 866 Processing helix chain 'a' and resid 884 through 888 removed outlier: 3.656A pdb=" N ALA a 887 " --> pdb=" O SER a 884 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE a 888 " --> pdb=" O PHE a 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 884 through 888' Processing helix chain 'b' and resid 222 through 246 removed outlier: 3.705A pdb=" N ILE b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL b 229 " --> pdb=" O MET b 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA b 231 " --> pdb=" O LEU b 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU b 234 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN b 246 " --> pdb=" O SER b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 250 through 254 removed outlier: 3.588A pdb=" N ALA b 253 " --> pdb=" O THR b 250 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 39 Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.694A pdb=" N ILE c 45 " --> pdb=" O GLY c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 90 removed outlier: 3.904A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL c 72 " --> pdb=" O VAL c 68 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY c 74 " --> pdb=" O LEU c 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP c 77 " --> pdb=" O VAL c 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER c 85 " --> pdb=" O ILE c 81 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET c 86 " --> pdb=" O THR c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 97 removed outlier: 3.635A pdb=" N ILE c 96 " --> pdb=" O ALA c 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR c 97 " --> pdb=" O PRO c 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 97' Processing helix chain 'c' and resid 98 through 100 No H-bonds generated for 'chain 'c' and resid 98 through 100' Processing helix chain 'c' and resid 101 through 123 removed outlier: 3.588A pdb=" N CYS c 107 " --> pdb=" O SER c 103 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE c 112 " --> pdb=" O GLU c 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY c 114 " --> pdb=" O VAL c 110 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL c 120 " --> pdb=" O ILE c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 removed outlier: 3.793A pdb=" N LEU c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL c 152 " --> pdb=" O ALA c 148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER c 155 " --> pdb=" O THR c 151 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA c 170 " --> pdb=" O THR c 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE c 172 " --> pdb=" O ALA c 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA c 175 " --> pdb=" O ALA c 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 192 removed outlier: 4.130A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 192 through 206 removed outlier: 4.023A pdb=" N LEU c 196 " --> pdb=" O SER c 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA c 206 " --> pdb=" O GLY c 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 9 removed outlier: 4.017A pdb=" N ILE d 8 " --> pdb=" O TYR d 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP d 9 " --> pdb=" O PHE d 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 5 through 9' Processing helix chain 'd' and resid 10 through 22 removed outlier: 3.533A pdb=" N GLY d 15 " --> pdb=" O GLY d 11 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN d 22 " --> pdb=" O ARG d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 35 removed outlier: 3.631A pdb=" N LEU d 33 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 86 removed outlier: 3.515A pdb=" N ILE d 68 " --> pdb=" O THR d 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN d 69 " --> pdb=" O THR d 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN d 86 " --> pdb=" O TYR d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 111 removed outlier: 4.323A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 141 removed outlier: 3.523A pdb=" N LEU d 139 " --> pdb=" O LEU d 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER d 140 " --> pdb=" O PRO d 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL d 141 " --> pdb=" O THR d 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 136 through 141' Processing helix chain 'd' and resid 145 through 150 Processing helix chain 'd' and resid 158 through 162 removed outlier: 3.600A pdb=" N PHE d 162 " --> pdb=" O ALA d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 removed outlier: 3.784A pdb=" N ILE d 177 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE d 179 " --> pdb=" O MET d 175 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 227 removed outlier: 3.991A pdb=" N CYS d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET d 208 " --> pdb=" O ALA d 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU d 211 " --> pdb=" O CYS d 207 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU d 215 " --> pdb=" O LEU d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 239 Processing helix chain 'd' and resid 248 through 258 removed outlier: 5.360A pdb=" N PHE d 254 " --> pdb=" O PRO d 250 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 267 removed outlier: 3.538A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 283 through 298 removed outlier: 3.786A pdb=" N ASP d 298 " --> pdb=" O GLU d 294 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 330 removed outlier: 4.318A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER d 315 " --> pdb=" O ALA d 311 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 23 removed outlier: 4.122A pdb=" N VAL e 10 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 54 removed outlier: 4.376A pdb=" N SER e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 39 " --> pdb=" O SER e 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 33 removed outlier: 3.635A pdb=" N LEU f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 71 removed outlier: 3.689A pdb=" N VAL f 51 " --> pdb=" O ASP f 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU f 57 " --> pdb=" O HIS f 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA f 58 " --> pdb=" O THR f 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE f 71 " --> pdb=" O VAL f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 43 removed outlier: 4.144A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER g 35 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 45 No H-bonds generated for 'chain 'g' and resid 44 through 45' Processing helix chain 'g' and resid 46 through 50 removed outlier: 3.638A pdb=" N LEU g 49 " --> pdb=" O ARG g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 76 removed outlier: 3.524A pdb=" N VAL g 70 " --> pdb=" O TYR g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 122 removed outlier: 3.823A pdb=" N VAL g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP g 113 " --> pdb=" O GLY g 109 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA g 114 " --> pdb=" O ILE g 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 153 removed outlier: 4.121A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU g 141 " --> pdb=" O GLU g 137 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL g 146 " --> pdb=" O TYR g 142 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG g 153 " --> pdb=" O LEU g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 43 removed outlier: 3.925A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA h 20 " --> pdb=" O GLY h 16 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER h 35 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY h 38 " --> pdb=" O LYS h 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 50 removed outlier: 3.766A pdb=" N LEU h 49 " --> pdb=" O ARG h 46 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 76 removed outlier: 4.079A pdb=" N ILE h 63 " --> pdb=" O MET h 59 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA h 64 " --> pdb=" O ALA h 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE h 65 " --> pdb=" O GLY h 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL h 70 " --> pdb=" O TYR h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 117 removed outlier: 4.006A pdb=" N SER h 100 " --> pdb=" O SER h 96 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA h 103 " --> pdb=" O LEU h 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG h 117 " --> pdb=" O ASP h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 155 removed outlier: 4.294A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE h 135 " --> pdb=" O LEU h 131 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG h 153 " --> pdb=" O LEU h 149 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR h 155 " --> pdb=" O ASN h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 43 removed outlier: 4.418A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER i 35 " --> pdb=" O GLY i 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 50 removed outlier: 3.736A pdb=" N LEU i 50 " --> pdb=" O PRO i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 75 removed outlier: 3.772A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA i 64 " --> pdb=" O ALA i 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL i 70 " --> pdb=" O TYR i 66 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS i 75 " --> pdb=" O SER i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 78 No H-bonds generated for 'chain 'i' and resid 76 through 78' Processing helix chain 'i' and resid 83 through 119 removed outlier: 3.574A pdb=" N VAL i 97 " --> pdb=" O ALA i 93 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA i 103 " --> pdb=" O LEU i 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA i 114 " --> pdb=" O ILE i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 152 removed outlier: 4.421A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 43 removed outlier: 4.429A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE j 23 " --> pdb=" O SER j 19 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 76 removed outlier: 3.723A pdb=" N ILE j 63 " --> pdb=" O MET j 59 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 117 removed outlier: 3.573A pdb=" N VAL j 97 " --> pdb=" O ALA j 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER j 100 " --> pdb=" O SER j 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA j 103 " --> pdb=" O LEU j 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 122 through 124 No H-bonds generated for 'chain 'j' and resid 122 through 124' Processing helix chain 'j' and resid 125 through 152 removed outlier: 3.664A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY j 143 " --> pdb=" O LEU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 42 removed outlier: 4.427A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA k 20 " --> pdb=" O GLY k 16 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER k 35 " --> pdb=" O GLY k 31 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE k 39 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 76 removed outlier: 3.526A pdb=" N ALA k 60 " --> pdb=" O PRO k 56 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE k 63 " --> pdb=" O MET k 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA k 64 " --> pdb=" O ALA k 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL k 70 " --> pdb=" O TYR k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 119 removed outlier: 3.814A pdb=" N SER k 100 " --> pdb=" O SER k 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 118 " --> pdb=" O ALA k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 122 through 124 No H-bonds generated for 'chain 'k' and resid 122 through 124' Processing helix chain 'k' and resid 125 through 151 removed outlier: 3.518A pdb=" N ILE k 130 " --> pdb=" O PHE k 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU k 131 " --> pdb=" O VAL k 127 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE k 135 " --> pdb=" O LEU k 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY k 143 " --> pdb=" O LEU k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 152 through 154 No H-bonds generated for 'chain 'k' and resid 152 through 154' Processing helix chain 'l' and resid 9 through 43 removed outlier: 3.999A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE l 23 " --> pdb=" O SER l 19 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER l 35 " --> pdb=" O GLY l 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.529A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU l 50 " --> pdb=" O PRO l 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 46 through 50' Processing helix chain 'l' and resid 54 through 74 removed outlier: 3.996A pdb=" N ILE l 63 " --> pdb=" O MET l 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA l 64 " --> pdb=" O ALA l 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE l 65 " --> pdb=" O GLY l 61 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY l 67 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 75 through 78 removed outlier: 3.540A pdb=" N LEU l 78 " --> pdb=" O CYS l 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 75 through 78' Processing helix chain 'l' and resid 83 through 117 removed outlier: 3.875A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA l 103 " --> pdb=" O LEU l 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP l 113 " --> pdb=" O GLY l 109 " (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: 3.748A pdb=" N PHE l 135 " --> pdb=" O LEU l 131 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 40 removed outlier: 4.393A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA m 20 " --> pdb=" O GLY m 16 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY m 27 " --> pdb=" O PHE m 23 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR m 30 " --> pdb=" O LEU m 26 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER m 35 " --> pdb=" O GLY m 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 50 Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.959A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL m 70 " --> pdb=" O TYR m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 117 removed outlier: 3.839A pdb=" N SER m 100 " --> pdb=" O SER m 96 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA m 103 " --> pdb=" O LEU m 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA m 114 " --> pdb=" O ILE m 110 " (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 152 removed outlier: 3.623A pdb=" N PHE m 135 " --> pdb=" O LEU m 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU m 141 " --> pdb=" O GLU m 137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY m 143 " --> pdb=" O LEU m 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 43 removed outlier: 4.175A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER n 35 " --> pdb=" O GLY n 31 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 46 through 50 removed outlier: 3.560A pdb=" N LEU n 49 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 76 removed outlier: 3.916A pdb=" N ILE n 63 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA n 64 " --> pdb=" O ALA n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 120 removed outlier: 4.015A pdb=" N SER n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA n 103 " --> pdb=" O LEU n 99 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP n 113 " --> pdb=" O GLY n 109 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA n 114 " --> pdb=" O ILE n 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER n 120 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 152 removed outlier: 4.503A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 4.373A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY o 19 " --> pdb=" O ALA o 15 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER o 41 " --> pdb=" O GLY o 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY o 44 " --> pdb=" O LYS o 40 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE o 48 " --> pdb=" O GLY o 44 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 56 removed outlier: 3.515A pdb=" N LEU o 55 " --> pdb=" O LYS o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 82 removed outlier: 3.527A pdb=" N SER o 66 " --> pdb=" O PRO o 62 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU o 69 " --> pdb=" O MET o 65 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA o 70 " --> pdb=" O SER o 66 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE o 71 " --> pdb=" O GLY o 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL o 76 " --> pdb=" O TYR o 72 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 128 removed outlier: 3.576A pdb=" N VAL o 105 " --> pdb=" O CYS o 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE o 107 " --> pdb=" O LEU o 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA o 108 " --> pdb=" O CYS o 104 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP o 121 " --> pdb=" O GLY o 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL o 124 " --> pdb=" O GLY o 120 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET o 128 " --> pdb=" O VAL o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 162 removed outlier: 4.382A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU o 149 " --> pdb=" O GLU o 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'a' and resid 267 through 270 removed outlier: 3.519A pdb=" N PHE a 269 " --> pdb=" O CYS a 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY a 242 " --> pdb=" O PHE a 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 540 through 541 Processing sheet with id=AA4, first strand: chain 'a' and resid 552 through 553 1429 hydrogen bonds defined for protein. 4236 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: 3.75 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6321 1.34 - 1.46: 4361 1.46 - 1.58: 10800 1.58 - 1.70: 1 1.70 - 1.82: 205 Bond restraints: 21688 Sorted by residual: bond pdb=" C ALA g 9 " pdb=" N PRO g 10 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.07e+01 bond pdb=" CB THR i 24 " pdb=" CG2 THR i 24 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.11e+00 bond pdb=" CA VAL g 55 " pdb=" C VAL g 55 " ideal model delta sigma weight residual 1.520 1.538 -0.019 8.80e-03 1.29e+04 4.45e+00 bond pdb=" C VAL a 691 " pdb=" N PRO a 692 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.00e+00 bond pdb=" CB THR g 24 " pdb=" CG2 THR g 24 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 ... (remaining 21683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 29055 3.15 - 6.31: 337 6.31 - 9.46: 60 9.46 - 12.62: 12 12.62 - 15.77: 3 Bond angle restraints: 29467 Sorted by residual: angle pdb=" C ILE l 54 " pdb=" N VAL l 55 " pdb=" CA VAL l 55 " ideal model delta sigma weight residual 120.24 125.38 -5.14 6.30e-01 2.52e+00 6.66e+01 angle pdb=" C ILE m 54 " pdb=" N VAL m 55 " pdb=" CA VAL m 55 " ideal model delta sigma weight residual 120.24 123.89 -3.65 6.30e-01 2.52e+00 3.36e+01 angle pdb=" N VAL f 39 " pdb=" CA VAL f 39 " pdb=" C VAL f 39 " ideal model delta sigma weight residual 113.53 108.13 5.40 9.80e-01 1.04e+00 3.04e+01 angle pdb=" C ILE g 54 " pdb=" N VAL g 55 " pdb=" CA VAL g 55 " ideal model delta sigma weight residual 120.24 123.62 -3.38 6.30e-01 2.52e+00 2.87e+01 angle pdb=" C GLN i 156 " pdb=" N ASP i 157 " pdb=" CA ASP i 157 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 ... (remaining 29462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 11951 15.21 - 30.41: 506 30.41 - 45.61: 102 45.61 - 60.82: 10 60.82 - 76.02: 13 Dihedral angle restraints: 12582 sinusoidal: 4552 harmonic: 8030 Sorted by residual: dihedral pdb=" CA TYR d 249 " pdb=" C TYR d 249 " pdb=" N PRO d 250 " pdb=" CA PRO d 250 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU d 172 " pdb=" C LEU d 172 " pdb=" N ASP d 173 " pdb=" CA ASP d 173 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA SER d 59 " pdb=" C SER d 59 " pdb=" N SER d 60 " pdb=" CA SER d 60 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 12579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3055 0.073 - 0.146: 461 0.146 - 0.219: 28 0.219 - 0.293: 6 0.293 - 0.366: 1 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CB ILE a 528 " pdb=" CA ILE a 528 " pdb=" CG1 ILE a 528 " pdb=" CG2 ILE a 528 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CG LEU c 199 " pdb=" CB LEU c 199 " pdb=" CD1 LEU c 199 " pdb=" CD2 LEU c 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE a 25 " pdb=" CA ILE a 25 " pdb=" CG1 ILE a 25 " pdb=" CG2 ILE a 25 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 3548 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 693 " 0.017 2.00e-02 2.50e+03 1.84e-02 8.50e+00 pdb=" CG TRP a 693 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP a 693 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 693 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 693 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP a 693 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 693 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 693 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 693 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP a 693 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " 0.017 2.00e-02 2.50e+03 1.83e-02 8.35e+00 pdb=" CG TRP c 77 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 192 " -0.019 2.00e-02 2.50e+03 2.13e-02 7.92e+00 pdb=" CG PHE d 192 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE d 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE d 192 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE d 192 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE d 192 " -0.001 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6110 2.82 - 3.34: 20102 3.34 - 3.86: 36565 3.86 - 4.38: 43475 4.38 - 4.90: 74398 Nonbonded interactions: 180650 Sorted by model distance: nonbonded pdb=" O GLY h 31 " pdb=" OG SER h 35 " model vdw 2.294 3.040 nonbonded pdb=" O ALA a 453 " pdb=" OG1 THR a 457 " model vdw 2.324 3.040 nonbonded pdb=" O GLY k 31 " pdb=" OG SER k 35 " model vdw 2.324 3.040 nonbonded pdb=" OG SER d 315 " pdb=" OH TYR d 345 " model vdw 2.330 3.040 nonbonded pdb=" O GLY g 31 " pdb=" OG SER g 35 " model vdw 2.332 3.040 ... (remaining 180645 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 'g' selection = (chain 'h' and resid 4 through 156) selection = (chain 'i' and resid 4 through 156) selection = (chain 'j' and resid 4 through 156) selection = (chain 'k' and resid 4 through 156) selection = (chain 'l' and resid 4 through 156) selection = (chain 'm' and resid 4 through 156) selection = (chain 'n' and resid 4 through 156) } 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: 1.040 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21688 Z= 0.245 Angle : 0.977 15.771 29467 Z= 0.533 Chirality : 0.053 0.366 3551 Planarity : 0.007 0.062 3641 Dihedral : 9.818 76.024 7480 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % 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: -3.98 (0.12), residues: 2794 helix: -2.27 (0.09), residues: 2042 sheet: -2.75 (0.73), residues: 45 loop : -3.15 (0.18), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 219 TYR 0.039 0.002 TYR a 605 PHE 0.049 0.003 PHE d 192 TRP 0.048 0.004 TRP a 693 HIS 0.023 0.003 HIS a 789 Details of bonding type rmsd covalent geometry : bond 0.00564 (21688) covalent geometry : angle 0.97677 (29467) hydrogen bonds : bond 0.14303 ( 1429) hydrogen bonds : angle 6.17032 ( 4236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 435 time to evaluate : 0.799 Fit side-chains REVERT: a 19 TYR cc_start: 0.8438 (t80) cc_final: 0.7889 (t80) REVERT: a 34 LYS cc_start: 0.8161 (mttp) cc_final: 0.7711 (mmtt) REVERT: a 72 ASN cc_start: 0.8238 (t160) cc_final: 0.7918 (m-40) REVERT: a 73 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7216 (mt-10) REVERT: a 258 ARG cc_start: 0.7522 (mtt90) cc_final: 0.7048 (mtm-85) REVERT: a 362 LYS cc_start: 0.7927 (mmpt) cc_final: 0.7476 (mtmt) REVERT: a 434 GLN cc_start: 0.7759 (tt0) cc_final: 0.7412 (pt0) REVERT: a 609 ASN cc_start: 0.7728 (t0) cc_final: 0.7332 (m-40) REVERT: a 622 LEU cc_start: 0.8169 (tm) cc_final: 0.7939 (tp) REVERT: a 678 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8594 (ptmt) REVERT: a 822 LYS cc_start: 0.8172 (mptp) cc_final: 0.7482 (mmmt) REVERT: c 24 LEU cc_start: 0.8448 (tp) cc_final: 0.8100 (tt) REVERT: c 132 ASN cc_start: 0.7881 (p0) cc_final: 0.7629 (p0) REVERT: c 196 LEU cc_start: 0.8848 (tm) cc_final: 0.8592 (tp) REVERT: d 79 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8294 (mt-10) REVERT: d 95 MET cc_start: 0.8722 (mmm) cc_final: 0.8423 (mmt) REVERT: d 186 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7960 (tttp) REVERT: d 206 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7197 (tt0) REVERT: d 217 ASP cc_start: 0.8081 (m-30) cc_final: 0.7789 (m-30) REVERT: d 254 PHE cc_start: 0.7765 (t80) cc_final: 0.7313 (t80) REVERT: d 286 ASP cc_start: 0.7993 (m-30) cc_final: 0.7701 (m-30) REVERT: d 297 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7867 (ttp-170) REVERT: d 340 ASN cc_start: 0.8011 (t160) cc_final: 0.7593 (t0) REVERT: g 7 VAL cc_start: 0.9037 (p) cc_final: 0.8681 (t) REVERT: h 49 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8469 (pp) REVERT: h 113 ASP cc_start: 0.8771 (t70) cc_final: 0.8560 (t70) REVERT: i 52 LYS cc_start: 0.8867 (tttt) cc_final: 0.8616 (tttp) REVERT: i 110 ILE cc_start: 0.8617 (tt) cc_final: 0.8217 (mt) REVERT: i 124 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8573 (mtp180) REVERT: l 19 SER cc_start: 0.9021 (t) cc_final: 0.8582 (m) REVERT: o 27 MET cc_start: 0.8631 (tpt) cc_final: 0.8316 (tpt) REVERT: o 118 MET cc_start: 0.8327 (mmm) cc_final: 0.8062 (mmt) REVERT: o 132 ARG cc_start: 0.8906 (mtp180) cc_final: 0.8672 (mtp180) outliers start: 2 outliers final: 0 residues processed: 437 average time/residue: 0.1820 time to fit residues: 117.1448 Evaluate side-chains 285 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 72 ASN a 117 ASN a 353 GLN a 437 GLN a 680 GLN a 767 ASN a 775 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 ASN c 46 ASN c 100 ASN d 128 HIS d 283 ASN d 303 GLN d 333 ASN d 340 ASN e 55 GLN j 53 ASN k 151 ASN l 122 GLN n 121 GLN ** o 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092961 restraints weight = 22623.985| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.48 r_work: 0.2802 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21688 Z= 0.122 Angle : 0.549 11.343 29467 Z= 0.283 Chirality : 0.039 0.199 3551 Planarity : 0.004 0.044 3641 Dihedral : 4.717 25.302 3010 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.43 % Allowed : 6.23 % Favored : 92.34 % 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: -1.69 (0.15), residues: 2794 helix: -0.53 (0.11), residues: 2068 sheet: -2.31 (0.76), residues: 41 loop : -2.54 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 161 TYR 0.012 0.001 TYR a 525 PHE 0.028 0.001 PHE c 80 TRP 0.023 0.002 TRP a 693 HIS 0.006 0.001 HIS a 789 Details of bonding type rmsd covalent geometry : bond 0.00268 (21688) covalent geometry : angle 0.54906 (29467) hydrogen bonds : bond 0.04051 ( 1429) hydrogen bonds : angle 4.04826 ( 4236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 0.690 Fit side-chains REVERT: a 19 TYR cc_start: 0.8602 (t80) cc_final: 0.8040 (t80) REVERT: a 34 LYS cc_start: 0.8113 (mttp) cc_final: 0.7562 (mmtt) REVERT: a 72 ASN cc_start: 0.7762 (t0) cc_final: 0.7538 (m-40) REVERT: a 73 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7491 (mt-10) REVERT: a 141 ARG cc_start: 0.6765 (tpp80) cc_final: 0.6529 (tpp-160) REVERT: a 258 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7332 (mtm-85) REVERT: a 307 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6667 (pp) REVERT: a 308 ASN cc_start: 0.7420 (m110) cc_final: 0.7152 (m-40) REVERT: a 362 LYS cc_start: 0.8090 (mmpt) cc_final: 0.7555 (mtmt) REVERT: a 434 GLN cc_start: 0.8180 (tt0) cc_final: 0.7901 (tt0) REVERT: a 472 MET cc_start: 0.8755 (mtp) cc_final: 0.8489 (mtm) REVERT: a 533 MET cc_start: 0.9137 (mtm) cc_final: 0.8914 (mtm) REVERT: a 609 ASN cc_start: 0.7920 (t0) cc_final: 0.7426 (m-40) REVERT: a 613 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8050 (t0) REVERT: a 641 SER cc_start: 0.8854 (m) cc_final: 0.8649 (m) REVERT: a 678 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8500 (ptmt) REVERT: a 784 LEU cc_start: 0.7825 (tt) cc_final: 0.7620 (tp) REVERT: a 822 LYS cc_start: 0.8166 (mptp) cc_final: 0.7324 (mmmt) REVERT: c 53 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8391 (mtp-110) REVERT: c 99 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8151 (pttt) REVERT: d 103 MET cc_start: 0.8989 (mtt) cc_final: 0.8718 (mtp) REVERT: d 146 GLU cc_start: 0.8049 (tp30) cc_final: 0.7710 (tt0) REVERT: d 206 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7551 (tt0) REVERT: d 251 LEU cc_start: 0.8231 (mt) cc_final: 0.8031 (mm) REVERT: d 286 ASP cc_start: 0.8282 (m-30) cc_final: 0.8019 (m-30) REVERT: d 293 MET cc_start: 0.8807 (mmm) cc_final: 0.8561 (mmm) REVERT: e 63 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7667 (mtm110) REVERT: h 46 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8167 (mtp180) REVERT: h 49 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (pp) REVERT: h 129 MET cc_start: 0.8687 (ttp) cc_final: 0.8212 (tmm) REVERT: i 110 ILE cc_start: 0.8716 (tt) cc_final: 0.8281 (mt) REVERT: i 124 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8588 (mtp180) REVERT: l 19 SER cc_start: 0.9037 (t) cc_final: 0.8727 (p) REVERT: m 131 LEU cc_start: 0.8852 (tp) cc_final: 0.8559 (tp) REVERT: o 132 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8718 (mtp180) REVERT: o 145 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8668 (tp30) outliers start: 32 outliers final: 10 residues processed: 332 average time/residue: 0.1626 time to fit residues: 81.9290 Evaluate side-chains 287 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 613 ASP Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 45 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 526 ASN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN c 132 ASN d 164 ASN d 333 ASN m 122 GLN o 94 ASN o 98 HIS o 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.090864 restraints weight = 22674.550| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.45 r_work: 0.2636 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 21688 Z= 0.276 Angle : 0.663 10.256 29467 Z= 0.335 Chirality : 0.045 0.203 3551 Planarity : 0.004 0.046 3641 Dihedral : 4.753 24.876 3010 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 7.93 % Favored : 89.56 % 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: -1.03 (0.15), residues: 2794 helix: -0.05 (0.11), residues: 2067 sheet: -2.34 (0.71), residues: 45 loop : -2.27 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 219 TYR 0.022 0.002 TYR o 127 PHE 0.039 0.002 PHE c 80 TRP 0.027 0.002 TRP a 693 HIS 0.010 0.002 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00689 (21688) covalent geometry : angle 0.66317 (29467) hydrogen bonds : bond 0.04667 ( 1429) hydrogen bonds : angle 4.16566 ( 4236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 0.776 Fit side-chains REVERT: a 19 TYR cc_start: 0.8635 (t80) cc_final: 0.8397 (t80) REVERT: a 34 LYS cc_start: 0.8109 (mttp) cc_final: 0.7554 (mmtt) REVERT: a 72 ASN cc_start: 0.7736 (t0) cc_final: 0.7478 (m-40) REVERT: a 73 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7337 (mt-10) REVERT: a 258 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7437 (mtm-85) REVERT: a 307 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7464 (pp) REVERT: a 308 ASN cc_start: 0.7879 (m110) cc_final: 0.7559 (m-40) REVERT: a 325 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6515 (tt) REVERT: a 362 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7547 (mtmt) REVERT: a 434 GLN cc_start: 0.8320 (tt0) cc_final: 0.7976 (tt0) REVERT: a 609 ASN cc_start: 0.7947 (t0) cc_final: 0.7464 (m-40) REVERT: a 611 LYS cc_start: 0.7510 (mptp) cc_final: 0.6416 (mmtt) REVERT: a 622 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (tp) REVERT: a 678 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8487 (ptmt) REVERT: b 246 ASN cc_start: 0.9030 (m-40) cc_final: 0.8789 (m110) REVERT: c 133 MET cc_start: 0.9252 (tpt) cc_final: 0.8970 (tpt) REVERT: d 206 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7712 (tt0) REVERT: d 251 LEU cc_start: 0.8477 (mt) cc_final: 0.8272 (mm) REVERT: d 286 ASP cc_start: 0.8345 (m-30) cc_final: 0.8100 (m-30) REVERT: e 63 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7306 (ttp80) REVERT: h 49 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8246 (pp) REVERT: h 129 MET cc_start: 0.8726 (ttp) cc_final: 0.8270 (tmm) REVERT: i 19 SER cc_start: 0.8935 (t) cc_final: 0.8461 (m) REVERT: i 52 LYS cc_start: 0.8799 (tttt) cc_final: 0.8501 (tttp) REVERT: i 110 ILE cc_start: 0.8910 (tt) cc_final: 0.8622 (mt) REVERT: k 5 CYS cc_start: 0.9020 (p) cc_final: 0.8780 (p) REVERT: n 59 MET cc_start: 0.8968 (mtp) cc_final: 0.8672 (mtt) REVERT: n 144 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (tp) REVERT: o 58 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8743 (ttmt) REVERT: o 145 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8772 (tp30) outliers start: 56 outliers final: 30 residues processed: 320 average time/residue: 0.1707 time to fit residues: 82.3760 Evaluate side-chains 298 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 285 ASP Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 334 ARG Chi-restraints excluded: chain a residue 336 LEU Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 622 LEU Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 100 ASN Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 159 VAL Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 144 LEU Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 272 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 235 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN c 132 ASN i 121 GLN i 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.090923 restraints weight = 22485.984| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.47 r_work: 0.2694 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21688 Z= 0.120 Angle : 0.506 8.715 29467 Z= 0.263 Chirality : 0.039 0.200 3551 Planarity : 0.003 0.044 3641 Dihedral : 4.408 24.711 3010 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 8.87 % Favored : 89.06 % 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: -0.23 (0.16), residues: 2794 helix: 0.54 (0.12), residues: 2065 sheet: -1.93 (0.72), residues: 45 loop : -1.99 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 161 TYR 0.011 0.001 TYR a 525 PHE 0.024 0.001 PHE c 80 TRP 0.014 0.001 TRP d 312 HIS 0.005 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00272 (21688) covalent geometry : angle 0.50592 (29467) hydrogen bonds : bond 0.03766 ( 1429) hydrogen bonds : angle 3.74486 ( 4236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.752 Fit side-chains REVERT: a 19 TYR cc_start: 0.8653 (t80) cc_final: 0.8262 (t80) REVERT: a 34 LYS cc_start: 0.7859 (mttp) cc_final: 0.7295 (mmtt) REVERT: a 72 ASN cc_start: 0.7579 (t0) cc_final: 0.7368 (m-40) REVERT: a 73 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7301 (mt-10) REVERT: a 258 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7376 (mtm-85) REVERT: a 307 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7363 (pp) REVERT: a 308 ASN cc_start: 0.7490 (m110) cc_final: 0.7274 (m-40) REVERT: a 325 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6403 (tt) REVERT: a 362 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7435 (mtmt) REVERT: a 390 THR cc_start: 0.8405 (m) cc_final: 0.8077 (p) REVERT: a 434 GLN cc_start: 0.8235 (tt0) cc_final: 0.7902 (tt0) REVERT: a 609 ASN cc_start: 0.7916 (t0) cc_final: 0.7451 (m-40) REVERT: a 613 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8017 (t0) REVERT: a 678 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8432 (ptmt) REVERT: a 822 LYS cc_start: 0.7823 (mmtp) cc_final: 0.6940 (mmmt) REVERT: b 246 ASN cc_start: 0.9024 (m-40) cc_final: 0.8735 (m110) REVERT: c 46 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8629 (t0) REVERT: c 99 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8322 (ttpt) REVERT: c 132 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7776 (p0) REVERT: c 133 MET cc_start: 0.8975 (tpt) cc_final: 0.8718 (tpt) REVERT: d 95 MET cc_start: 0.8711 (mmt) cc_final: 0.8434 (mmt) REVERT: d 206 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7584 (tt0) REVERT: d 251 LEU cc_start: 0.8372 (mt) cc_final: 0.8132 (mm) REVERT: d 286 ASP cc_start: 0.8249 (m-30) cc_final: 0.8019 (m-30) REVERT: e 63 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7474 (ttp80) REVERT: h 49 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8191 (pp) REVERT: h 129 MET cc_start: 0.8627 (ttp) cc_final: 0.8214 (tmm) REVERT: i 68 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8231 (tp) REVERT: i 110 ILE cc_start: 0.8738 (tt) cc_final: 0.8368 (mt) REVERT: k 5 CYS cc_start: 0.8978 (p) cc_final: 0.8678 (p) REVERT: l 19 SER cc_start: 0.9090 (t) cc_final: 0.8727 (p) REVERT: n 42 THR cc_start: 0.8812 (t) cc_final: 0.8598 (t) REVERT: n 59 MET cc_start: 0.8803 (mtp) cc_final: 0.8554 (mtt) outliers start: 46 outliers final: 18 residues processed: 299 average time/residue: 0.1677 time to fit residues: 75.7222 Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 334 ARG Chi-restraints excluded: chain a residue 421 LYS Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 613 ASP Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 99 LYS Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN d 318 GLN d 333 ASN n 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.090859 restraints weight = 22514.389| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.44 r_work: 0.2619 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 21688 Z= 0.227 Angle : 0.586 9.653 29467 Z= 0.298 Chirality : 0.042 0.177 3551 Planarity : 0.004 0.045 3641 Dihedral : 4.490 25.367 3010 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.42 % Allowed : 9.32 % Favored : 88.26 % 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: -0.13 (0.16), residues: 2794 helix: 0.59 (0.11), residues: 2073 sheet: -1.87 (0.72), residues: 45 loop : -1.91 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG o 161 TYR 0.014 0.001 TYR o 127 PHE 0.034 0.002 PHE c 80 TRP 0.016 0.002 TRP a 693 HIS 0.008 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00562 (21688) covalent geometry : angle 0.58616 (29467) hydrogen bonds : bond 0.04260 ( 1429) hydrogen bonds : angle 3.90449 ( 4236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.761 Fit side-chains REVERT: a 19 TYR cc_start: 0.8657 (t80) cc_final: 0.8420 (t80) REVERT: a 34 LYS cc_start: 0.8022 (mttp) cc_final: 0.7499 (mmtt) REVERT: a 72 ASN cc_start: 0.7649 (t0) cc_final: 0.7440 (m-40) REVERT: a 73 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7257 (mt-10) REVERT: a 258 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7327 (mtm-85) REVERT: a 307 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7673 (pp) REVERT: a 308 ASN cc_start: 0.7780 (m110) cc_final: 0.7522 (m-40) REVERT: a 325 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6541 (tt) REVERT: a 360 MET cc_start: 0.7646 (tmm) cc_final: 0.7425 (ttp) REVERT: a 362 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7504 (mtmt) REVERT: a 434 GLN cc_start: 0.8238 (tt0) cc_final: 0.7910 (tt0) REVERT: a 571 THR cc_start: 0.8668 (m) cc_final: 0.8468 (p) REVERT: a 609 ASN cc_start: 0.7892 (t0) cc_final: 0.7429 (m-40) REVERT: a 678 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8371 (ptpt) REVERT: b 246 ASN cc_start: 0.9060 (m-40) cc_final: 0.8715 (m-40) REVERT: c 46 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8752 (t0) REVERT: c 99 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8282 (ttpt) REVERT: c 132 ASN cc_start: 0.8278 (p0) cc_final: 0.7915 (p0) REVERT: c 133 MET cc_start: 0.9186 (tpt) cc_final: 0.8977 (tpt) REVERT: d 206 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7638 (tt0) REVERT: d 251 LEU cc_start: 0.8522 (mt) cc_final: 0.8272 (mm) REVERT: d 286 ASP cc_start: 0.8292 (m-30) cc_final: 0.8027 (m-30) REVERT: e 63 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7561 (ttp80) REVERT: h 49 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8235 (pp) REVERT: h 129 MET cc_start: 0.8693 (ttp) cc_final: 0.8232 (tmm) REVERT: i 19 SER cc_start: 0.8879 (t) cc_final: 0.8459 (m) REVERT: i 110 ILE cc_start: 0.8790 (tt) cc_final: 0.8484 (mt) REVERT: l 68 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8288 (tp) REVERT: n 42 THR cc_start: 0.8833 (t) cc_final: 0.8612 (t) REVERT: n 59 MET cc_start: 0.8895 (mtp) cc_final: 0.8633 (mtt) REVERT: o 145 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8677 (tp30) outliers start: 54 outliers final: 36 residues processed: 298 average time/residue: 0.1659 time to fit residues: 74.9808 Evaluate side-chains 295 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 285 ASP Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 334 ARG Chi-restraints excluded: chain a residue 336 LEU Chi-restraints excluded: chain a residue 421 LYS Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 99 LYS Chi-restraints excluded: chain c residue 100 ASN Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 313 MET Chi-restraints excluded: chain e residue 23 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 159 VAL Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 0.0000 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095078 restraints weight = 22228.169| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.46 r_work: 0.2689 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21688 Z= 0.116 Angle : 0.495 8.443 29467 Z= 0.256 Chirality : 0.039 0.235 3551 Planarity : 0.003 0.043 3641 Dihedral : 4.242 24.782 3010 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.93 % Allowed : 10.00 % Favored : 88.08 % 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: 0.40 (0.16), residues: 2794 helix: 0.98 (0.12), residues: 2075 sheet: -1.66 (0.69), residues: 47 loop : -1.76 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.013 0.001 TYR a 525 PHE 0.022 0.001 PHE c 80 TRP 0.012 0.001 TRP d 312 HIS 0.005 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00266 (21688) covalent geometry : angle 0.49480 (29467) hydrogen bonds : bond 0.03607 ( 1429) hydrogen bonds : angle 3.63429 ( 4236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.802 Fit side-chains REVERT: a 19 TYR cc_start: 0.8639 (t80) cc_final: 0.8235 (t80) REVERT: a 34 LYS cc_start: 0.7845 (mttp) cc_final: 0.7363 (mmtt) REVERT: a 73 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7274 (mt-10) REVERT: a 258 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7248 (mtm-85) REVERT: a 307 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7470 (pp) REVERT: a 308 ASN cc_start: 0.7721 (m110) cc_final: 0.7466 (m-40) REVERT: a 325 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6315 (tt) REVERT: a 362 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7423 (mtmt) REVERT: a 390 THR cc_start: 0.8439 (m) cc_final: 0.8168 (p) REVERT: a 434 GLN cc_start: 0.8204 (tt0) cc_final: 0.7865 (tt0) REVERT: a 609 ASN cc_start: 0.7863 (t0) cc_final: 0.7384 (m-40) REVERT: a 678 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8351 (ptmt) REVERT: a 822 LYS cc_start: 0.7783 (mmtp) cc_final: 0.6921 (mmmt) REVERT: b 246 ASN cc_start: 0.9105 (m-40) cc_final: 0.8778 (m-40) REVERT: c 99 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: c 100 ASN cc_start: 0.8797 (t0) cc_final: 0.8536 (m-40) REVERT: c 132 ASN cc_start: 0.7841 (p0) cc_final: 0.7567 (p0) REVERT: c 133 MET cc_start: 0.8990 (tpt) cc_final: 0.8736 (tpt) REVERT: d 206 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7596 (tt0) REVERT: d 286 ASP cc_start: 0.8245 (m-30) cc_final: 0.7999 (m-30) REVERT: e 63 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7562 (ttp80) REVERT: h 49 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8185 (pp) REVERT: h 113 ASP cc_start: 0.9092 (t70) cc_final: 0.8873 (t70) REVERT: h 129 MET cc_start: 0.8619 (ttp) cc_final: 0.8212 (tmm) REVERT: i 68 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8220 (tp) REVERT: i 110 ILE cc_start: 0.8746 (tt) cc_final: 0.8356 (mt) REVERT: l 19 SER cc_start: 0.9092 (t) cc_final: 0.8742 (p) REVERT: l 52 LYS cc_start: 0.8145 (tttt) cc_final: 0.7927 (ttpt) REVERT: n 42 THR cc_start: 0.8764 (t) cc_final: 0.8534 (t) outliers start: 43 outliers final: 24 residues processed: 287 average time/residue: 0.1670 time to fit residues: 71.9625 Evaluate side-chains 279 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 138 ASP Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 336 LEU Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 421 LYS Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 99 LYS Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 23 ILE Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 202 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 255 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 263 ASN a 353 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.090401 restraints weight = 22472.504| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.48 r_work: 0.2683 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21688 Z= 0.123 Angle : 0.495 8.407 29467 Z= 0.254 Chirality : 0.039 0.204 3551 Planarity : 0.003 0.042 3641 Dihedral : 4.124 24.484 3010 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 10.09 % Favored : 87.85 % 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: 0.66 (0.16), residues: 2794 helix: 1.18 (0.12), residues: 2076 sheet: -1.52 (0.70), residues: 47 loop : -1.69 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.012 0.001 TYR a 525 PHE 0.025 0.001 PHE c 80 TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00292 (21688) covalent geometry : angle 0.49523 (29467) hydrogen bonds : bond 0.03563 ( 1429) hydrogen bonds : angle 3.57406 ( 4236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.610 Fit side-chains REVERT: a 19 TYR cc_start: 0.8667 (t80) cc_final: 0.8295 (t80) REVERT: a 34 LYS cc_start: 0.7811 (mttp) cc_final: 0.7332 (mmtt) REVERT: a 258 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7230 (mtm-85) REVERT: a 362 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7377 (mtmt) REVERT: a 390 THR cc_start: 0.8456 (m) cc_final: 0.8205 (p) REVERT: a 434 GLN cc_start: 0.8185 (tt0) cc_final: 0.7836 (tt0) REVERT: a 609 ASN cc_start: 0.7845 (t0) cc_final: 0.7367 (m-40) REVERT: a 613 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8027 (t0) REVERT: a 678 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8361 (ptmt) REVERT: a 822 LYS cc_start: 0.7784 (mmtp) cc_final: 0.6905 (mmmt) REVERT: b 246 ASN cc_start: 0.9105 (m-40) cc_final: 0.8842 (m110) REVERT: c 99 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8152 (ttpt) REVERT: c 132 ASN cc_start: 0.7870 (p0) cc_final: 0.7595 (p0) REVERT: c 133 MET cc_start: 0.8999 (tpt) cc_final: 0.8742 (tpt) REVERT: d 206 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7559 (tt0) REVERT: d 286 ASP cc_start: 0.8299 (m-30) cc_final: 0.8042 (m-30) REVERT: e 63 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7546 (ttp80) REVERT: h 49 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8231 (pp) REVERT: h 129 MET cc_start: 0.8610 (ttp) cc_final: 0.8207 (tmm) REVERT: i 68 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8180 (tp) REVERT: i 110 ILE cc_start: 0.8741 (tt) cc_final: 0.8351 (mt) REVERT: l 19 SER cc_start: 0.9093 (t) cc_final: 0.8750 (p) REVERT: l 52 LYS cc_start: 0.8143 (tttt) cc_final: 0.7926 (ttpt) REVERT: l 68 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8239 (tp) REVERT: n 42 THR cc_start: 0.8765 (t) cc_final: 0.8539 (t) REVERT: o 65 MET cc_start: 0.8716 (mtp) cc_final: 0.8344 (mtt) outliers start: 46 outliers final: 28 residues processed: 288 average time/residue: 0.1641 time to fit residues: 72.6204 Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 285 ASP Chi-restraints excluded: chain a residue 334 ARG Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 613 ASP Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 99 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 75 CYS Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 4 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 195 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.088102 restraints weight = 22590.008| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.53 r_work: 0.2698 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21688 Z= 0.112 Angle : 0.484 8.310 29467 Z= 0.249 Chirality : 0.038 0.196 3551 Planarity : 0.003 0.044 3641 Dihedral : 4.036 24.254 3010 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 10.53 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2794 helix: 1.34 (0.12), residues: 2084 sheet: -1.23 (0.72), residues: 47 loop : -1.62 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.012 0.001 TYR a 525 PHE 0.024 0.001 PHE c 80 TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00257 (21688) covalent geometry : angle 0.48379 (29467) hydrogen bonds : bond 0.03423 ( 1429) hydrogen bonds : angle 3.49316 ( 4236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.972 Fit side-chains REVERT: a 19 TYR cc_start: 0.8604 (t80) cc_final: 0.8127 (t80) REVERT: a 34 LYS cc_start: 0.7785 (mttp) cc_final: 0.7310 (mmtt) REVERT: a 258 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7215 (mtm-85) REVERT: a 362 LYS cc_start: 0.7907 (mmpt) cc_final: 0.7357 (mtmt) REVERT: a 390 THR cc_start: 0.8433 (m) cc_final: 0.8192 (p) REVERT: a 434 GLN cc_start: 0.8152 (tt0) cc_final: 0.7793 (tt0) REVERT: a 583 MET cc_start: 0.8699 (ttp) cc_final: 0.8367 (ttm) REVERT: a 609 ASN cc_start: 0.7820 (t0) cc_final: 0.7335 (m-40) REVERT: a 613 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8050 (t0) REVERT: a 678 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8319 (ptmt) REVERT: a 822 LYS cc_start: 0.7806 (mmtp) cc_final: 0.6923 (mmmt) REVERT: b 221 GLU cc_start: 0.7361 (pt0) cc_final: 0.6918 (pm20) REVERT: c 132 ASN cc_start: 0.7786 (p0) cc_final: 0.7520 (p0) REVERT: c 133 MET cc_start: 0.8980 (tpt) cc_final: 0.8736 (tpt) REVERT: d 206 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7590 (tt0) REVERT: d 286 ASP cc_start: 0.8274 (m-30) cc_final: 0.7992 (m-30) REVERT: e 63 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7514 (ttp80) REVERT: g 7 VAL cc_start: 0.9122 (p) cc_final: 0.8759 (t) REVERT: h 49 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8204 (pp) REVERT: h 129 MET cc_start: 0.8588 (ttp) cc_final: 0.8198 (tmm) REVERT: i 68 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8148 (tp) REVERT: i 110 ILE cc_start: 0.8714 (tt) cc_final: 0.8311 (mt) REVERT: l 19 SER cc_start: 0.9071 (t) cc_final: 0.8763 (p) REVERT: l 52 LYS cc_start: 0.8097 (tttt) cc_final: 0.7890 (ttpt) REVERT: l 68 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8212 (tp) REVERT: n 42 THR cc_start: 0.8750 (t) cc_final: 0.8525 (t) REVERT: o 57 MET cc_start: 0.9245 (mmm) cc_final: 0.9042 (mmm) REVERT: o 65 MET cc_start: 0.8685 (mtp) cc_final: 0.8313 (mtt) outliers start: 40 outliers final: 32 residues processed: 283 average time/residue: 0.1588 time to fit residues: 68.3624 Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 285 ASP Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 613 ASP Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 75 CYS Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 270 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** 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 = 0.3291 r_free = 0.3291 target = 0.117370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.086700 restraints weight = 22631.336| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.53 r_work: 0.2675 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.003 0.065 21688 Z= 0.135 Angle : 0.502 8.471 29467 Z= 0.257 Chirality : 0.039 0.200 3551 Planarity : 0.003 0.040 3641 Dihedral : 4.053 24.329 3010 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.75 % Allowed : 10.94 % Favored : 87.32 % 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: 0.95 (0.16), residues: 2794 helix: 1.38 (0.12), residues: 2080 sheet: -1.08 (0.73), residues: 47 loop : -1.62 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.012 0.001 TYR a 525 PHE 0.026 0.001 PHE c 80 TRP 0.009 0.001 TRP d 310 HIS 0.004 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00325 (21688) covalent geometry : angle 0.50217 (29467) hydrogen bonds : bond 0.03573 ( 1429) hydrogen bonds : angle 3.54404 ( 4236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.740 Fit side-chains REVERT: a 19 TYR cc_start: 0.8593 (t80) cc_final: 0.7765 (t80) REVERT: a 34 LYS cc_start: 0.7917 (mttp) cc_final: 0.7421 (mmtt) REVERT: a 258 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7149 (mtm-85) REVERT: a 362 LYS cc_start: 0.8098 (mmpt) cc_final: 0.7472 (mtmt) REVERT: a 390 THR cc_start: 0.8553 (m) cc_final: 0.8306 (p) REVERT: a 434 GLN cc_start: 0.8172 (tt0) cc_final: 0.7824 (tt0) REVERT: a 583 MET cc_start: 0.8714 (ttp) cc_final: 0.8370 (ttm) REVERT: a 609 ASN cc_start: 0.7829 (t0) cc_final: 0.7365 (m-40) REVERT: a 678 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8326 (ptmt) REVERT: a 822 LYS cc_start: 0.7816 (mmtp) cc_final: 0.6889 (mmmt) REVERT: b 221 GLU cc_start: 0.7436 (pt0) cc_final: 0.6977 (pm20) REVERT: c 132 ASN cc_start: 0.7904 (p0) cc_final: 0.7623 (p0) REVERT: c 133 MET cc_start: 0.8994 (tpt) cc_final: 0.8736 (tpt) REVERT: d 174 ASP cc_start: 0.8494 (t0) cc_final: 0.8274 (m-30) REVERT: d 206 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7687 (tt0) REVERT: d 286 ASP cc_start: 0.8298 (m-30) cc_final: 0.8023 (m-30) REVERT: e 63 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7522 (ttp80) REVERT: h 49 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8225 (pp) REVERT: h 129 MET cc_start: 0.8610 (ttp) cc_final: 0.8202 (tmm) REVERT: i 68 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (tp) REVERT: i 110 ILE cc_start: 0.8721 (tt) cc_final: 0.8356 (mt) REVERT: l 19 SER cc_start: 0.9104 (t) cc_final: 0.8749 (p) REVERT: l 52 LYS cc_start: 0.8108 (tttt) cc_final: 0.7895 (ttpt) REVERT: l 68 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8222 (tp) REVERT: n 42 THR cc_start: 0.8769 (t) cc_final: 0.8538 (t) REVERT: o 65 MET cc_start: 0.8721 (mtp) cc_final: 0.8344 (mtt) outliers start: 39 outliers final: 32 residues processed: 270 average time/residue: 0.1628 time to fit residues: 66.9068 Evaluate side-chains 275 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 285 ASP Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 75 CYS Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 148 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.0170 chunk 95 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** 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 = 0.3330 r_free = 0.3330 target = 0.120437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.089802 restraints weight = 22574.872| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.54 r_work: 0.2711 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21688 Z= 0.102 Angle : 0.473 8.269 29467 Z= 0.243 Chirality : 0.038 0.190 3551 Planarity : 0.003 0.040 3641 Dihedral : 3.944 24.115 3010 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 10.76 % Favored : 87.54 % 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: 1.19 (0.16), residues: 2794 helix: 1.55 (0.12), residues: 2088 sheet: -0.77 (0.75), residues: 47 loop : -1.54 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.013 0.001 TYR a 525 PHE 0.022 0.001 PHE c 80 TRP 0.009 0.001 TRP e 48 HIS 0.003 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00228 (21688) covalent geometry : angle 0.47345 (29467) hydrogen bonds : bond 0.03278 ( 1429) hydrogen bonds : angle 3.41938 ( 4236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.692 Fit side-chains REVERT: a 19 TYR cc_start: 0.8578 (t80) cc_final: 0.8086 (t80) REVERT: a 34 LYS cc_start: 0.7771 (mttp) cc_final: 0.7283 (mmtt) REVERT: a 77 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7379 (ttpt) REVERT: a 141 ARG cc_start: 0.6720 (ttm110) cc_final: 0.6406 (ttm110) REVERT: a 258 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7058 (mtm-85) REVERT: a 362 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7413 (mtmt) REVERT: a 434 GLN cc_start: 0.8141 (tt0) cc_final: 0.7785 (tt0) REVERT: a 514 MET cc_start: 0.8891 (mtp) cc_final: 0.8686 (mtt) REVERT: a 541 GLN cc_start: 0.8728 (tt0) cc_final: 0.8413 (tt0) REVERT: a 583 MET cc_start: 0.8677 (ttp) cc_final: 0.8351 (ttm) REVERT: a 609 ASN cc_start: 0.7821 (t0) cc_final: 0.7354 (m-40) REVERT: a 613 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8019 (t0) REVERT: a 822 LYS cc_start: 0.7848 (mmtp) cc_final: 0.6936 (mmmt) REVERT: a 850 PHE cc_start: 0.8539 (m-80) cc_final: 0.8274 (m-80) REVERT: b 221 GLU cc_start: 0.7285 (pt0) cc_final: 0.6874 (pm20) REVERT: c 100 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.8923 (m110) REVERT: c 132 ASN cc_start: 0.7739 (p0) cc_final: 0.7468 (p0) REVERT: d 95 MET cc_start: 0.8704 (mmt) cc_final: 0.8380 (mmt) REVERT: d 206 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7664 (tt0) REVERT: d 286 ASP cc_start: 0.8263 (m-30) cc_final: 0.8031 (m-30) REVERT: e 63 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7549 (ttp80) REVERT: h 49 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8166 (pp) REVERT: h 129 MET cc_start: 0.8546 (ttp) cc_final: 0.8165 (tmm) REVERT: i 68 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8141 (tp) REVERT: i 110 ILE cc_start: 0.8659 (tt) cc_final: 0.8245 (mt) REVERT: l 19 SER cc_start: 0.9054 (t) cc_final: 0.8764 (p) REVERT: l 68 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8172 (tp) REVERT: n 42 THR cc_start: 0.8722 (t) cc_final: 0.8500 (t) REVERT: o 65 MET cc_start: 0.8655 (mtp) cc_final: 0.8295 (mtt) outliers start: 38 outliers final: 29 residues processed: 285 average time/residue: 0.1682 time to fit residues: 72.5938 Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 334 ARG Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 440 VAL Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 510 VAL Chi-restraints excluded: chain a residue 613 ASP Chi-restraints excluded: chain a residue 858 LEU Chi-restraints excluded: chain b residue 242 SER Chi-restraints excluded: chain c residue 100 ASN Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain d residue 340 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 49 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 75 CYS Chi-restraints excluded: chain n residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 265 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 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 569 HIS ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.085599 restraints weight = 22543.662| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.33 r_work: 0.2742 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21688 Z= 0.114 Angle : 0.487 8.387 29467 Z= 0.249 Chirality : 0.038 0.191 3551 Planarity : 0.003 0.039 3641 Dihedral : 3.932 24.231 3010 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.66 % Allowed : 10.98 % Favored : 87.36 % 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: 1.25 (0.16), residues: 2794 helix: 1.60 (0.12), residues: 2082 sheet: -0.63 (0.75), residues: 47 loop : -1.54 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 161 TYR 0.012 0.001 TYR a 525 PHE 0.024 0.001 PHE c 80 TRP 0.008 0.001 TRP d 310 HIS 0.004 0.001 HIS a 864 Details of bonding type rmsd covalent geometry : bond 0.00268 (21688) covalent geometry : angle 0.48680 (29467) hydrogen bonds : bond 0.03358 ( 1429) hydrogen bonds : angle 3.44123 ( 4236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.12 seconds wall clock time: 83 minutes 26.91 seconds (5006.91 seconds total)