Starting phenix.real_space_refine on Tue Apr 7 15:29:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwz_54352/04_2026/9rwz_54352.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 1.145 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 50 5.49 5 S 170 5.16 5 C 17865 2.51 5 N 5080 2.21 5 O 5434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28601 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6579 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 779 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "G" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 512 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 20} Chain: "H" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1447 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "I" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1452 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 173} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 547 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 21} Chain: "N" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7499 Classifications: {'peptide': 1013} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 952} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 392 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 5, 'HIS:plan': 6, 'TYR:plan': 6, 'ARG:plan': 9, 'ASP:plan': 6, 'TRP:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 260 Chain: "M" Number of atoms: 7475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7475 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 966} Chain breaks: 8 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ARG:plan': 12, 'ASN:plan1': 10, 'GLN:plan1': 15, 'HIS:plan': 14, 'GLU:plan': 6, 'TYR:plan': 6, 'ASP:plan': 7, 'PHE:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 364 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14593 SG CYS N 188 59.163 145.477 108.109 1.00 69.27 S ATOM 14606 SG CYS N 190 59.685 141.918 107.264 1.00 79.38 S ATOM 14653 SG CYS N 197 59.917 144.633 104.694 1.00 80.54 S ATOM 22038 SG CYS M 188 67.795 137.041 130.939 1.00 30.00 S ATOM 22051 SG CYS M 190 67.380 134.992 127.885 1.00 30.00 S ATOM 22098 SG CYS M 197 68.106 133.467 131.215 1.00 86.46 S Time building chain proxies: 5.51, per 1000 atoms: 0.19 Number of scatterers: 28601 At special positions: 0 Unit cell: (142.15, 228.973, 213.651, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 170 16.00 P 50 15.00 O 5434 8.00 N 5080 7.00 C 17865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M1901 " pdb="ZN ZN M1901 " - pdb=" SG CYS M 190 " pdb="ZN ZN M1901 " - pdb=" ND1 HIS M 199 " pdb="ZN ZN M1901 " - pdb=" SG CYS M 197 " pdb="ZN ZN M1901 " - pdb=" SG CYS M 188 " pdb=" ZN N1901 " pdb="ZN ZN N1901 " - pdb=" ND1 HIS N 199 " pdb="ZN ZN N1901 " - pdb=" SG CYS N 190 " pdb="ZN ZN N1901 " - pdb=" SG CYS N 188 " pdb="ZN ZN N1901 " - pdb=" SG CYS N 197 " Number of angles added : 6 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6858 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 15 sheets defined 57.6% alpha, 7.6% beta 19 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.653A pdb=" N SER A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.520A pdb=" N LYS A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.708A pdb=" N PHE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.713A pdb=" N ALA A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 removed outlier: 3.693A pdb=" N PHE A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.513A pdb=" N LEU A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.799A pdb=" N GLU A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.576A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.597A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 568 " --> pdb=" O CYS A 564 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.641A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 693 removed outlier: 3.506A pdb=" N HIS A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.557A pdb=" N LEU A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 removed outlier: 3.623A pdb=" N ARG A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.698A pdb=" N LEU A 853 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.703A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.584A pdb=" N GLU B 41 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 42 " --> pdb=" O PRO B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 42' Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.523A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.584A pdb=" N GLU C 41 " --> pdb=" O PRO C 38 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN C 42 " --> pdb=" O PRO C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 38 through 42' Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.701A pdb=" N MET D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 removed outlier: 4.139A pdb=" N THR D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 4.426A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.508A pdb=" N LEU E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.862A pdb=" N VAL E 81 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'H' and resid 26 through 45 removed outlier: 3.674A pdb=" N VAL H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 67 removed outlier: 3.804A pdb=" N HIS H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 96 removed outlier: 3.669A pdb=" N LEU H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.930A pdb=" N MET H 118 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 135 removed outlier: 3.594A pdb=" N ASP H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLN H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 154 through 175 Processing helix chain 'H' and resid 180 through 187 Processing helix chain 'I' and resid 26 through 46 removed outlier: 4.055A pdb=" N VAL I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 67 Processing helix chain 'I' and resid 70 through 88 removed outlier: 3.919A pdb=" N HIS I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 85 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE I 86 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 88 " --> pdb=" O HIS I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 100 through 123 removed outlier: 3.821A pdb=" N THR I 104 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU I 105 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET I 118 " --> pdb=" O THR I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 removed outlier: 4.101A pdb=" N VAL I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN I 132 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'I' and resid 157 through 174 removed outlier: 3.593A pdb=" N LEU I 166 " --> pdb=" O ARG I 162 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP I 167 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU I 172 " --> pdb=" O MET I 168 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG I 173 " --> pdb=" O ILE I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 188 Processing helix chain 'N' and resid 75 through 88 Processing helix chain 'N' and resid 89 through 94 removed outlier: 3.753A pdb=" N VAL N 93 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 111 Processing helix chain 'N' and resid 117 through 129 Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.074A pdb=" N GLN N 135 " --> pdb=" O ALA N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 210 removed outlier: 3.588A pdb=" N VAL N 201 " --> pdb=" O CYS N 197 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA N 202 " --> pdb=" O THR N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 225 Processing helix chain 'N' and resid 228 through 243 removed outlier: 3.585A pdb=" N GLU N 242 " --> pdb=" O TYR N 238 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU N 243 " --> pdb=" O LEU N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 246 No H-bonds generated for 'chain 'N' and resid 244 through 246' Processing helix chain 'N' and resid 247 through 260 removed outlier: 4.159A pdb=" N GLU N 257 " --> pdb=" O ARG N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 307 Processing helix chain 'N' and resid 315 through 324 Processing helix chain 'N' and resid 326 through 341 removed outlier: 4.016A pdb=" N ALA N 333 " --> pdb=" O ALA N 329 " (cutoff:3.500A) Proline residue: N 338 - end of helix Processing helix chain 'N' and resid 344 through 360 removed outlier: 3.671A pdb=" N TRP N 348 " --> pdb=" O PRO N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 379 removed outlier: 3.906A pdb=" N TYR N 379 " --> pdb=" O GLN N 375 " (cutoff:3.500A) Processing helix chain 'N' and resid 379 through 391 removed outlier: 3.888A pdb=" N THR N 383 " --> pdb=" O TYR N 379 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG N 390 " --> pdb=" O TRP N 386 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR N 391 " --> pdb=" O TYR N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 396 Processing helix chain 'N' and resid 411 through 431 removed outlier: 3.644A pdb=" N ALA N 415 " --> pdb=" O VAL N 411 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 417 " --> pdb=" O ALA N 413 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 431 " --> pdb=" O TRP N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 461 removed outlier: 3.607A pdb=" N CYS N 445 " --> pdb=" O ARG N 441 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR N 446 " --> pdb=" O ARG N 442 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN N 447 " --> pdb=" O GLU N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 475 through 483 removed outlier: 3.914A pdb=" N TYR N 483 " --> pdb=" O VAL N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 485 through 490 removed outlier: 3.562A pdb=" N ALA N 489 " --> pdb=" O ASN N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 763 through 767 removed outlier: 3.563A pdb=" N GLU N 767 " --> pdb=" O LEU N 764 " (cutoff:3.500A) Processing helix chain 'N' and resid 768 through 783 removed outlier: 3.652A pdb=" N PHE N 774 " --> pdb=" O MET N 770 " (cutoff:3.500A) Processing helix chain 'N' and resid 785 through 802 removed outlier: 3.818A pdb=" N ALA N 789 " --> pdb=" O TYR N 785 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU N 795 " --> pdb=" O ARG N 791 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA N 802 " --> pdb=" O GLN N 798 " (cutoff:3.500A) Processing helix chain 'N' and resid 823 through 844 removed outlier: 3.713A pdb=" N SER N 835 " --> pdb=" O THR N 831 " (cutoff:3.500A) Processing helix chain 'N' and resid 850 through 863 Processing helix chain 'N' and resid 871 through 890 Processing helix chain 'N' and resid 895 through 911 removed outlier: 3.708A pdb=" N SER N 900 " --> pdb=" O PRO N 896 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR N 901 " --> pdb=" O SER N 897 " (cutoff:3.500A) Processing helix chain 'N' and resid 923 through 934 removed outlier: 3.535A pdb=" N SER N 927 " --> pdb=" O LEU N 923 " (cutoff:3.500A) Processing helix chain 'N' and resid 952 through 965 removed outlier: 3.641A pdb=" N GLY N 965 " --> pdb=" O VAL N 961 " (cutoff:3.500A) Processing helix chain 'N' and resid 978 through 997 removed outlier: 3.688A pdb=" N THR N 982 " --> pdb=" O LEU N 978 " (cutoff:3.500A) Processing helix chain 'N' and resid 1003 through 1012 Processing helix chain 'N' and resid 1234 through 1253 removed outlier: 3.644A pdb=" N ALA N1238 " --> pdb=" O SER N1234 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY N1253 " --> pdb=" O LEU N1249 " (cutoff:3.500A) Processing helix chain 'N' and resid 1276 through 1296 removed outlier: 3.773A pdb=" N VAL N1295 " --> pdb=" O LEU N1291 " (cutoff:3.500A) Processing helix chain 'N' and resid 1298 through 1302 removed outlier: 3.891A pdb=" N SER N1301 " --> pdb=" O ASN N1298 " (cutoff:3.500A) Processing helix chain 'N' and resid 1308 through 1318 Processing helix chain 'N' and resid 1320 through 1334 removed outlier: 3.549A pdb=" N GLU N1328 " --> pdb=" O THR N1324 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS N1329 " --> pdb=" O ILE N1325 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP N1331 " --> pdb=" O VAL N1327 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY N1332 " --> pdb=" O GLU N1328 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS N1333 " --> pdb=" O CYS N1329 " (cutoff:3.500A) Processing helix chain 'N' and resid 1335 through 1348 removed outlier: 3.795A pdb=" N ALA N1340 " --> pdb=" O PRO N1336 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG N1348 " --> pdb=" O ASP N1344 " (cutoff:3.500A) Processing helix chain 'N' and resid 1353 through 1366 Processing helix chain 'N' and resid 1367 through 1369 No H-bonds generated for 'chain 'N' and resid 1367 through 1369' Processing helix chain 'N' and resid 1373 through 1386 removed outlier: 3.802A pdb=" N GLU N1386 " --> pdb=" O VAL N1382 " (cutoff:3.500A) Processing helix chain 'N' and resid 1389 through 1407 removed outlier: 4.842A pdb=" N GLY N1405 " --> pdb=" O GLU N1401 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY N1407 " --> pdb=" O ALA N1403 " (cutoff:3.500A) Processing helix chain 'N' and resid 1409 through 1429 Processing helix chain 'N' and resid 1663 through 1680 Processing helix chain 'N' and resid 1695 through 1711 removed outlier: 4.087A pdb=" N LYS N1709 " --> pdb=" O GLY N1705 " (cutoff:3.500A) Processing helix chain 'N' and resid 1714 through 1724 removed outlier: 4.235A pdb=" N PHE N1718 " --> pdb=" O TYR N1714 " (cutoff:3.500A) Processing helix chain 'N' and resid 1728 through 1743 Processing helix chain 'N' and resid 1755 through 1778 removed outlier: 3.578A pdb=" N HIS N1778 " --> pdb=" O HIS N1774 " (cutoff:3.500A) Processing helix chain 'N' and resid 1780 through 1798 removed outlier: 4.472A pdb=" N ASP N1785 " --> pdb=" O PRO N1781 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP N1786 " --> pdb=" O ALA N1782 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE N1798 " --> pdb=" O ALA N1794 " (cutoff:3.500A) Processing helix chain 'N' and resid 1801 through 1818 Processing helix chain 'M' and resid 75 through 87 removed outlier: 3.550A pdb=" N LEU M 79 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.621A pdb=" N VAL M 93 " --> pdb=" O PRO M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 111 removed outlier: 3.541A pdb=" N GLN M 105 " --> pdb=" O PRO M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 127 removed outlier: 3.582A pdb=" N ALA M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 143 removed outlier: 3.939A pdb=" N GLN M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 210 Processing helix chain 'M' and resid 219 through 225 Processing helix chain 'M' and resid 228 through 243 Processing helix chain 'M' and resid 247 through 259 Processing helix chain 'M' and resid 264 through 269 removed outlier: 3.766A pdb=" N VAL M 269 " --> pdb=" O ALA M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 307 Processing helix chain 'M' and resid 326 through 337 Processing helix chain 'M' and resid 344 through 360 removed outlier: 3.667A pdb=" N TRP M 348 " --> pdb=" O PRO M 344 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN M 349 " --> pdb=" O GLU M 345 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU M 350 " --> pdb=" O GLY M 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS M 359 " --> pdb=" O ARG M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 379 removed outlier: 4.334A pdb=" N TYR M 379 " --> pdb=" O GLN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 390 removed outlier: 3.976A pdb=" N THR M 383 " --> pdb=" O TYR M 379 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG M 390 " --> pdb=" O TRP M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 432 removed outlier: 3.566A pdb=" N HIS M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA M 415 " --> pdb=" O VAL M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 463 removed outlier: 4.159A pdb=" N GLY M 462 " --> pdb=" O ASN M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 482 Processing helix chain 'M' and resid 768 through 783 removed outlier: 4.047A pdb=" N ALA M 775 " --> pdb=" O GLU M 771 " (cutoff:3.500A) Processing helix chain 'M' and resid 785 through 803 removed outlier: 3.600A pdb=" N ARG M 791 " --> pdb=" O SER M 787 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN M 798 " --> pdb=" O VAL M 794 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP M 799 " --> pdb=" O GLU M 795 " (cutoff:3.500A) Processing helix chain 'M' and resid 823 through 845 removed outlier: 4.029A pdb=" N TRP M 828 " --> pdb=" O SER M 824 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL M 829 " --> pdb=" O ARG M 825 " (cutoff:3.500A) Processing helix chain 'M' and resid 852 through 863 Processing helix chain 'M' and resid 871 through 889 removed outlier: 3.517A pdb=" N GLU M 875 " --> pdb=" O THR M 871 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL M 876 " --> pdb=" O LYS M 872 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 877 " --> pdb=" O ALA M 873 " (cutoff:3.500A) Processing helix chain 'M' and resid 890 through 892 No H-bonds generated for 'chain 'M' and resid 890 through 892' Processing helix chain 'M' and resid 895 through 911 Processing helix chain 'M' and resid 922 through 934 removed outlier: 3.676A pdb=" N ALA M 926 " --> pdb=" O PRO M 922 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER M 927 " --> pdb=" O LEU M 923 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 965 removed outlier: 3.532A pdb=" N GLY M 965 " --> pdb=" O VAL M 961 " (cutoff:3.500A) Processing helix chain 'M' and resid 975 through 997 removed outlier: 4.329A pdb=" N CYS M 979 " --> pdb=" O HIS M 975 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU M 980 " --> pdb=" O PRO M 976 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY M 981 " --> pdb=" O LEU M 977 " (cutoff:3.500A) Processing helix chain 'M' and resid 1003 through 1012 removed outlier: 3.800A pdb=" N LYS M1010 " --> pdb=" O LYS M1006 " (cutoff:3.500A) Processing helix chain 'M' and resid 1234 through 1252 removed outlier: 3.621A pdb=" N ALA M1238 " --> pdb=" O SER M1234 " (cutoff:3.500A) Processing helix chain 'M' and resid 1277 through 1296 removed outlier: 3.606A pdb=" N PHE M1282 " --> pdb=" O HIS M1278 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU M1283 " --> pdb=" O LEU M1279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE M1284 " --> pdb=" O CYS M1280 " (cutoff:3.500A) Processing helix chain 'M' and resid 1298 through 1302 removed outlier: 3.807A pdb=" N SER M1301 " --> pdb=" O ASN M1298 " (cutoff:3.500A) Processing helix chain 'M' and resid 1305 through 1315 removed outlier: 4.236A pdb=" N GLY M1313 " --> pdb=" O SER M1309 " (cutoff:3.500A) Processing helix chain 'M' and resid 1319 through 1327 removed outlier: 4.099A pdb=" N LEU M1323 " --> pdb=" O GLY M1319 " (cutoff:3.500A) Processing helix chain 'M' and resid 1335 through 1347 removed outlier: 3.573A pdb=" N SER M1347 " --> pdb=" O ALA M1343 " (cutoff:3.500A) Processing helix chain 'M' and resid 1353 through 1365 removed outlier: 3.730A pdb=" N ALA M1357 " --> pdb=" O ASN M1353 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS M1365 " --> pdb=" O LEU M1361 " (cutoff:3.500A) Processing helix chain 'M' and resid 1366 through 1369 Processing helix chain 'M' and resid 1373 through 1386 removed outlier: 3.528A pdb=" N CYS M1384 " --> pdb=" O ALA M1380 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS M1385 " --> pdb=" O LEU M1381 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU M1386 " --> pdb=" O VAL M1382 " (cutoff:3.500A) Processing helix chain 'M' and resid 1389 through 1404 removed outlier: 4.161A pdb=" N LYS M1404 " --> pdb=" O GLU M1400 " (cutoff:3.500A) Processing helix chain 'M' and resid 1409 through 1424 removed outlier: 3.538A pdb=" N LEU M1413 " --> pdb=" O TYR M1409 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU M1423 " --> pdb=" O GLN M1419 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR M1424 " --> pdb=" O TRP M1420 " (cutoff:3.500A) Processing helix chain 'M' and resid 1657 through 1662 removed outlier: 3.597A pdb=" N LEU M1661 " --> pdb=" O ASN M1657 " (cutoff:3.500A) Processing helix chain 'M' and resid 1662 through 1682 Processing helix chain 'M' and resid 1692 through 1704 removed outlier: 3.844A pdb=" N TYR M1696 " --> pdb=" O ARG M1692 " (cutoff:3.500A) Processing helix chain 'M' and resid 1705 through 1709 Processing helix chain 'M' and resid 1713 through 1726 removed outlier: 3.530A pdb=" N VAL M1726 " --> pdb=" O ALA M1722 " (cutoff:3.500A) Processing helix chain 'M' and resid 1728 through 1743 Processing helix chain 'M' and resid 1755 through 1778 removed outlier: 3.742A pdb=" N ILE M1777 " --> pdb=" O HIS M1773 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS M1778 " --> pdb=" O HIS M1774 " (cutoff:3.500A) Processing helix chain 'M' and resid 1780 through 1782 No H-bonds generated for 'chain 'M' and resid 1780 through 1782' Processing helix chain 'M' and resid 1783 through 1799 Processing helix chain 'M' and resid 1801 through 1817 Processing helix chain 'M' and resid 1821 through 1835 removed outlier: 4.227A pdb=" N TRP M1825 " --> pdb=" O THR M1821 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 631 removed outlier: 5.653A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 669 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 598 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.821A pdb=" N PHE A 200 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 400 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.531A pdb=" N SER A 136 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS A 62 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 130 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 130 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 346 removed outlier: 3.515A pdb=" N ASN A 345 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 281 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A 331 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N CYS A 327 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A 338 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.546A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 73 through 75 removed outlier: 6.250A pdb=" N PHE B 4 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 75 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET B 6 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 15 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS E 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 11.665A pdb=" N ASP B 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 75 removed outlier: 8.665A pdb=" N ALA C 73 " --> pdb=" O ASP C 2 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 13 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LYS D 32 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N PHE C 15 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB4, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 183 through 188 removed outlier: 4.179A pdb=" N THR N 159 " --> pdb=" O ASP N 148 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP N 148 " --> pdb=" O THR N 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS N 215 " --> pdb=" O PRO N 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 183 through 187 removed outlier: 3.694A pdb=" N SER M 185 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR M 159 " --> pdb=" O ASP M 148 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP M 148 " --> pdb=" O THR M 159 " (cutoff:3.500A) 1486 hydrogen bonds defined for protein. 4365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4936 1.32 - 1.44: 7668 1.44 - 1.57: 16340 1.57 - 1.69: 98 1.69 - 1.82: 254 Bond restraints: 29296 Sorted by residual: bond pdb=" CA SER N 397 " pdb=" CB SER N 397 " ideal model delta sigma weight residual 1.534 1.468 0.066 1.45e-02 4.76e+03 2.09e+01 bond pdb=" CA SER N 399 " pdb=" CB SER N 399 " ideal model delta sigma weight residual 1.534 1.461 0.073 1.65e-02 3.67e+03 1.95e+01 bond pdb=" CA ALA N 398 " pdb=" CB ALA N 398 " ideal model delta sigma weight residual 1.528 1.471 0.057 1.39e-02 5.18e+03 1.70e+01 bond pdb=" CA SER N 392 " pdb=" CB SER N 392 " ideal model delta sigma weight residual 1.534 1.463 0.071 1.76e-02 3.23e+03 1.64e+01 bond pdb=" CA SER N 396 " pdb=" CB SER N 396 " ideal model delta sigma weight residual 1.536 1.458 0.078 2.01e-02 2.48e+03 1.49e+01 ... (remaining 29291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 38875 1.72 - 3.44: 920 3.44 - 5.16: 180 5.16 - 6.88: 26 6.88 - 8.59: 7 Bond angle restraints: 40008 Sorted by residual: angle pdb=" C VAL M1382 " pdb=" CA VAL M1382 " pdb=" CB VAL M1382 " ideal model delta sigma weight residual 112.26 104.45 7.81 1.62e+00 3.81e-01 2.32e+01 angle pdb=" C THR D 88 " pdb=" CA THR D 88 " pdb=" CB THR D 88 " ideal model delta sigma weight residual 115.79 110.16 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" CA ASP M1388 " pdb=" C ASP M1388 " pdb=" O ASP M1388 " ideal model delta sigma weight residual 119.97 115.66 4.31 9.40e-01 1.13e+00 2.10e+01 angle pdb=" N CYS M1384 " pdb=" CA CYS M1384 " pdb=" C CYS M1384 " ideal model delta sigma weight residual 112.45 118.81 -6.36 1.39e+00 5.18e-01 2.10e+01 angle pdb=" N SER N 399 " pdb=" CA SER N 399 " pdb=" C SER N 399 " ideal model delta sigma weight residual 108.52 101.82 6.70 1.52e+00 4.33e-01 1.94e+01 ... (remaining 40003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 16575 17.75 - 35.51: 916 35.51 - 53.26: 214 53.26 - 71.02: 71 71.02 - 88.77: 19 Dihedral angle restraints: 17795 sinusoidal: 7264 harmonic: 10531 Sorted by residual: dihedral pdb=" CA ARG H 46 " pdb=" C ARG H 46 " pdb=" N LYS H 47 " pdb=" CA LYS H 47 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N GLU A 683 " pdb=" CA GLU A 683 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY A 301 " pdb=" C GLY A 301 " pdb=" N GLN A 302 " pdb=" CA GLN A 302 " ideal model delta harmonic sigma weight residual -180.00 -159.62 -20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 17792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4366 0.097 - 0.195: 197 0.195 - 0.292: 7 0.292 - 0.389: 0 0.389 - 0.487: 1 Chirality restraints: 4571 Sorted by residual: chirality pdb=" CA VAL M 809 " pdb=" N VAL M 809 " pdb=" C VAL M 809 " pdb=" CB VAL M 809 " both_signs ideal model delta sigma weight residual False 2.44 2.93 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA GLU M1386 " pdb=" N GLU M1386 " pdb=" C GLU M1386 " pdb=" CB GLU M1386 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1' A G 5 " pdb=" O4' A G 5 " pdb=" C2' A G 5 " pdb=" N9 A G 5 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4568 not shown) Planarity restraints: 5032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 64 " -0.028 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C GLU A 64 " 0.098 2.00e-02 2.50e+03 pdb=" O GLU A 64 " -0.038 2.00e-02 2.50e+03 pdb=" N LYS A 65 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER N 388 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C SER N 388 " 0.069 2.00e-02 2.50e+03 pdb=" O SER N 388 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL N 389 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP N1330 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C TRP N1330 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP N1330 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP N1331 " 0.016 2.00e-02 2.50e+03 ... (remaining 5029 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 502 2.68 - 3.23: 27383 3.23 - 3.79: 42209 3.79 - 4.34: 53631 4.34 - 4.90: 90032 Nonbonded interactions: 213757 Sorted by model distance: nonbonded pdb=" OD1 ASN N 852 " pdb=" OE2 GLU N 898 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU E 54 " pdb=" OG SER I 53 " model vdw 2.132 3.040 nonbonded pdb=" O SER B 21 " pdb=" OG1 THR B 56 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 478 " pdb=" O MET A 483 " model vdw 2.174 3.040 nonbonded pdb=" OG SER M 130 " pdb=" OE1 GLU M 133 " model vdw 2.201 3.040 ... (remaining 213752 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 14 through 112) selection = chain 'E' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 16 through 189) } ncs_group { reference = (chain 'M' and (resid 71 through 164 or resid 171 through 937 or resid 951 throu \ gh 1014 or (resid 1015 and (name N or name CA or name C or name O or name CB )) \ or resid 1227 through 1253 or resid 1270 through 1426 or resid 1656 through 1682 \ or (resid 1694 through 1704 and (name N or name CA or name C or name O or name \ CB )) or resid 1705 through 1823 or resid 1901)) selection = (chain 'N' and (resid 71 through 164 or resid 171 through 309 or resid 324 throu \ gh 401 or (resid 402 and (name N or name CA or name C or name O or name CB )) or \ resid 403 or (resid 404 through 406 and (name N or name CA or name C or name O \ or name CB )) or resid 407 or (resid 408 through 409 and (name N or name CA or n \ ame C or name O or name CB )) or resid 410 through 462 or (resid 463 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 4 \ 99 or resid 758 through 814 or (resid 815 and (name N or name CA or name C or na \ me O or name CB )) or resid 816 or (resid 817 through 821 and (name N or name CA \ or name C or name O or name CB )) or resid 822 through 1426 or (resid 1656 thro \ ugh 1670 and (name N or name CA or name C or name O or name CB )) or resid 1671 \ through 1901)) } 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: 19.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.500 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.231 29304 Z= 0.335 Angle : 0.663 9.921 40014 Z= 0.374 Chirality : 0.046 0.487 4571 Planarity : 0.006 0.060 5032 Dihedral : 12.466 88.769 10937 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 1.28 % Allowed : 6.50 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.09 (0.14), residues: 3555 helix: 1.36 (0.12), residues: 1908 sheet: 0.43 (0.30), residues: 310 loop : -2.03 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 983 TYR 0.017 0.002 TYR I 62 PHE 0.019 0.002 PHE A 202 TRP 0.025 0.003 TRP A 451 HIS 0.005 0.001 HIS N 155 Details of bonding type rmsd covalent geometry : bond 0.00732 (29296) covalent geometry : angle 0.65722 (40008) hydrogen bonds : bond 0.15171 ( 1531) hydrogen bonds : angle 5.34630 ( 4455) metal coordination : bond 0.11416 ( 8) metal coordination : angle 6.94444 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 712 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8070 (tt0) cc_final: 0.7837 (tp30) REVERT: A 115 LEU cc_start: 0.8521 (mt) cc_final: 0.7978 (mt) REVERT: A 127 ILE cc_start: 0.8661 (mm) cc_final: 0.8234 (mm) REVERT: A 129 LYS cc_start: 0.8465 (mttp) cc_final: 0.8248 (mtpp) REVERT: A 131 SER cc_start: 0.8374 (m) cc_final: 0.8076 (p) REVERT: A 213 MET cc_start: 0.8676 (mmm) cc_final: 0.8407 (mmm) REVERT: A 260 LYS cc_start: 0.8235 (mtpt) cc_final: 0.8018 (mtpt) REVERT: A 283 ASN cc_start: 0.8745 (t0) cc_final: 0.8337 (t0) REVERT: A 332 GLN cc_start: 0.8141 (mt0) cc_final: 0.7703 (mt0) REVERT: A 366 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7968 (mtm-85) REVERT: A 383 MET cc_start: 0.8231 (tmm) cc_final: 0.7914 (tpp) REVERT: A 395 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: A 425 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8109 (mmtm) REVERT: A 447 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 472 GLU cc_start: 0.7668 (tp30) cc_final: 0.7414 (tp30) REVERT: A 628 THR cc_start: 0.8469 (m) cc_final: 0.8142 (p) REVERT: A 683 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 756 ILE cc_start: 0.8832 (mt) cc_final: 0.8566 (mm) REVERT: A 850 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7648 (tm-30) REVERT: E 17 MET cc_start: 0.7150 (ttm) cc_final: 0.6744 (tpp) REVERT: H 33 ILE cc_start: 0.8210 (mm) cc_final: 0.7936 (mm) REVERT: H 60 ASN cc_start: 0.8346 (m-40) cc_final: 0.8045 (m-40) REVERT: H 118 MET cc_start: 0.6984 (mmp) cc_final: 0.6711 (mmt) REVERT: H 148 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.6721 (mmt90) REVERT: I 78 ARG cc_start: 0.6076 (mtm-85) cc_final: 0.5857 (mtm-85) REVERT: N 133 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6800 (mt-10) REVERT: N 433 ASP cc_start: 0.8038 (p0) cc_final: 0.7699 (p0) REVERT: N 898 GLU cc_start: 0.7310 (mp0) cc_final: 0.7078 (mp0) REVERT: N 1241 TYR cc_start: 0.8634 (m-80) cc_final: 0.8379 (m-80) REVERT: N 1303 THR cc_start: 0.8901 (p) cc_final: 0.8690 (m) REVERT: M 77 VAL cc_start: 0.8439 (t) cc_final: 0.8229 (m) REVERT: M 139 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7760 (tm-30) REVERT: M 147 LYS cc_start: 0.8621 (mttt) cc_final: 0.8378 (mmtm) REVERT: M 165 MET cc_start: 0.6976 (tpp) cc_final: 0.6774 (tpp) REVERT: M 245 GLN cc_start: 0.7433 (mt0) cc_final: 0.7229 (mt0) REVERT: M 297 ASN cc_start: 0.7515 (m-40) cc_final: 0.7109 (m-40) REVERT: M 345 GLU cc_start: 0.7366 (tt0) cc_final: 0.7079 (tt0) REVERT: M 440 ARG cc_start: 0.8531 (mmm160) cc_final: 0.8297 (tpt90) REVERT: M 451 TRP cc_start: 0.8706 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: M 479 VAL cc_start: 0.8400 (t) cc_final: 0.8081 (m) REVERT: M 770 MET cc_start: 0.7845 (mmp) cc_final: 0.7586 (mmt) REVERT: M 771 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7486 (mm-30) REVERT: M 795 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7520 (tm-30) REVERT: M 799 ASP cc_start: 0.8122 (t70) cc_final: 0.7814 (t0) REVERT: M 927 SER cc_start: 0.8561 (t) cc_final: 0.8358 (m) REVERT: M 1324 THR cc_start: 0.9051 (t) cc_final: 0.8755 (m) REVERT: M 1415 GLU cc_start: 0.7927 (tp30) cc_final: 0.7667 (tp30) outliers start: 36 outliers final: 15 residues processed: 740 average time/residue: 0.2014 time to fit residues: 226.8129 Evaluate side-chains 644 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 628 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain N residue 399 SER Chi-restraints excluded: chain N residue 764 LEU Chi-restraints excluded: chain N residue 1007 ILE Chi-restraints excluded: chain N residue 1330 TRP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 451 TRP Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1379 ARG Chi-restraints excluded: chain M residue 1385 LYS Chi-restraints excluded: chain M residue 1386 GLU Chi-restraints excluded: chain M residue 1392 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 432 GLN A 558 GLN A 588 GLN A 788 HIS D 35 HIS E 35 HIS H 31 ASN H 69 HIS H 87 ASN H 134 ASN N 105 GLN N 116 ASN N 228 GLN N 395 HIS N 401 HIS N 458 ASN N 463 GLN ** N 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 975 HIS N1307 HIS N1370 HIS M 231 GLN M1298 ASN M1383 GLN M1389 ASN M1426 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.159070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120980 restraints weight = 42258.578| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.61 r_work: 0.3212 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29304 Z= 0.175 Angle : 0.565 6.691 40014 Z= 0.299 Chirality : 0.041 0.255 4571 Planarity : 0.005 0.053 5032 Dihedral : 10.669 91.224 4654 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.35 % Allowed : 12.33 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.50 (0.14), residues: 3555 helix: 1.63 (0.12), residues: 1963 sheet: 0.48 (0.29), residues: 322 loop : -1.88 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 33 TYR 0.020 0.001 TYR M1424 PHE 0.025 0.002 PHE I 147 TRP 0.017 0.002 TRP A 134 HIS 0.010 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00410 (29296) covalent geometry : angle 0.56410 (40008) hydrogen bonds : bond 0.05519 ( 1531) hydrogen bonds : angle 4.07244 ( 4455) metal coordination : bond 0.00672 ( 8) metal coordination : angle 2.51909 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 625 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8579 (tt0) cc_final: 0.8361 (tp30) REVERT: A 82 PHE cc_start: 0.8841 (m-80) cc_final: 0.8622 (m-80) REVERT: A 115 LEU cc_start: 0.8693 (mt) cc_final: 0.8406 (mt) REVERT: A 197 GLU cc_start: 0.8482 (tt0) cc_final: 0.8242 (tt0) REVERT: A 245 GLU cc_start: 0.8407 (mp0) cc_final: 0.7987 (mp0) REVERT: A 278 LYS cc_start: 0.8702 (mttt) cc_final: 0.8404 (mtmm) REVERT: A 332 GLN cc_start: 0.8133 (mt0) cc_final: 0.7908 (mt0) REVERT: A 383 MET cc_start: 0.8654 (tmm) cc_final: 0.8322 (tpp) REVERT: A 425 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8354 (mmtp) REVERT: A 447 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 472 GLU cc_start: 0.8430 (tp30) cc_final: 0.8151 (tp30) REVERT: A 683 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 756 ILE cc_start: 0.8892 (mt) cc_final: 0.8669 (mm) REVERT: A 850 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 17 MET cc_start: 0.7522 (ttm) cc_final: 0.7319 (ttm) REVERT: H 60 ASN cc_start: 0.8590 (m-40) cc_final: 0.8064 (m110) REVERT: H 118 MET cc_start: 0.7702 (mmp) cc_final: 0.7430 (mtt) REVERT: H 148 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.6920 (mmt90) REVERT: I 38 LYS cc_start: 0.8156 (tttt) cc_final: 0.7913 (tttt) REVERT: N 433 ASP cc_start: 0.8245 (p0) cc_final: 0.7990 (p0) REVERT: N 458 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7452 (t0) REVERT: N 799 ASP cc_start: 0.8238 (t70) cc_final: 0.7929 (t0) REVERT: N 898 GLU cc_start: 0.7961 (mp0) cc_final: 0.7209 (mp0) REVERT: N 931 ASP cc_start: 0.7833 (t0) cc_final: 0.7499 (t0) REVERT: N 958 GLU cc_start: 0.7420 (tp30) cc_final: 0.6887 (tp30) REVERT: N 1404 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8270 (ptpp) REVERT: M 77 VAL cc_start: 0.8497 (t) cc_final: 0.8277 (m) REVERT: M 147 LYS cc_start: 0.8600 (mttt) cc_final: 0.8290 (mttm) REVERT: M 165 MET cc_start: 0.7009 (tpp) cc_final: 0.6788 (tpp) REVERT: M 297 ASN cc_start: 0.7671 (m-40) cc_final: 0.7426 (m-40) REVERT: M 419 MET cc_start: 0.8718 (ttp) cc_final: 0.8392 (ptp) REVERT: M 440 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8249 (tpt90) REVERT: M 766 GLN cc_start: 0.7435 (pp30) cc_final: 0.6977 (pp30) REVERT: M 771 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7906 (mm-30) REVERT: M 795 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7796 (tm-30) REVERT: M 908 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8024 (tm-30) REVERT: M 927 SER cc_start: 0.8552 (t) cc_final: 0.8309 (m) REVERT: M 953 GLU cc_start: 0.7015 (mp0) cc_final: 0.6366 (mp0) REVERT: M 1009 ASP cc_start: 0.7809 (m-30) cc_final: 0.7418 (m-30) REVERT: M 1334 LEU cc_start: 0.7950 (mt) cc_final: 0.7750 (mt) REVERT: M 1378 GLN cc_start: 0.7444 (tp40) cc_final: 0.7164 (tp40) REVERT: M 1379 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7312 (mmm160) REVERT: M 1393 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: M 1415 GLU cc_start: 0.7887 (tp30) cc_final: 0.7324 (tp30) outliers start: 66 outliers final: 43 residues processed: 656 average time/residue: 0.2019 time to fit residues: 201.3105 Evaluate side-chains 650 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 604 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 458 ASN Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 1007 ILE Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1330 TRP Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1370 HIS Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 378 THR Chi-restraints excluded: chain M residue 476 ARG Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1379 ARG Chi-restraints excluded: chain M residue 1391 MET Chi-restraints excluded: chain M residue 1393 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 70 optimal weight: 0.9980 chunk 192 optimal weight: 0.0980 chunk 302 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 218 optimal weight: 0.0570 chunk 224 optimal weight: 0.0010 chunk 320 optimal weight: 1.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN D 35 HIS I 113 GLN N 116 ASN N 155 HIS ** N 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1307 HIS M1333 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.159652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121900 restraints weight = 42413.003| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.06 r_work: 0.3225 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29304 Z= 0.138 Angle : 0.522 6.621 40014 Z= 0.275 Chirality : 0.040 0.229 4571 Planarity : 0.005 0.052 5032 Dihedral : 10.417 88.776 4638 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.63 % Allowed : 13.15 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.72 (0.15), residues: 3555 helix: 1.82 (0.12), residues: 1977 sheet: 0.57 (0.29), residues: 320 loop : -1.84 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 791 TYR 0.016 0.001 TYR M1424 PHE 0.025 0.001 PHE I 147 TRP 0.013 0.001 TRP A 134 HIS 0.027 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00316 (29296) covalent geometry : angle 0.52131 (40008) hydrogen bonds : bond 0.04480 ( 1531) hydrogen bonds : angle 3.80458 ( 4455) metal coordination : bond 0.00573 ( 8) metal coordination : angle 1.91546 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 612 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.8776 (m-80) cc_final: 0.8482 (m-80) REVERT: A 115 LEU cc_start: 0.8745 (mt) cc_final: 0.8304 (mt) REVERT: A 172 MET cc_start: 0.8543 (mtt) cc_final: 0.8307 (mtp) REVERT: A 245 GLU cc_start: 0.8377 (mp0) cc_final: 0.7974 (mp0) REVERT: A 278 LYS cc_start: 0.8642 (mttt) cc_final: 0.8353 (mtmm) REVERT: A 370 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: A 378 GLU cc_start: 0.8163 (tt0) cc_final: 0.7708 (tt0) REVERT: A 383 MET cc_start: 0.8602 (tmm) cc_final: 0.8274 (tpp) REVERT: A 425 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8339 (mmtm) REVERT: A 447 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 472 GLU cc_start: 0.8358 (tp30) cc_final: 0.8077 (tp30) REVERT: A 756 ILE cc_start: 0.8872 (mt) cc_final: 0.8643 (mm) REVERT: A 850 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 851 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: D 34 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8264 (mm-30) REVERT: D 108 ASN cc_start: 0.8811 (t0) cc_final: 0.8531 (t0) REVERT: H 60 ASN cc_start: 0.8557 (m-40) cc_final: 0.8076 (m110) REVERT: H 118 MET cc_start: 0.7683 (mmp) cc_final: 0.7459 (mtt) REVERT: H 148 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6924 (mmt90) REVERT: I 38 LYS cc_start: 0.8159 (tttt) cc_final: 0.7891 (tttt) REVERT: I 39 ASN cc_start: 0.6826 (m-40) cc_final: 0.6564 (m-40) REVERT: I 59 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7702 (mtp-110) REVERT: I 168 MET cc_start: 0.4232 (mpp) cc_final: 0.3465 (tpp) REVERT: N 318 SER cc_start: 0.8504 (m) cc_final: 0.8147 (p) REVERT: N 433 ASP cc_start: 0.8241 (p0) cc_final: 0.7983 (p0) REVERT: N 898 GLU cc_start: 0.7936 (mp0) cc_final: 0.7335 (mp0) REVERT: N 931 ASP cc_start: 0.7866 (t0) cc_final: 0.7486 (t0) REVERT: N 958 GLU cc_start: 0.7464 (tp30) cc_final: 0.6920 (tp30) REVERT: N 961 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7847 (t) REVERT: N 1241 TYR cc_start: 0.8295 (m-80) cc_final: 0.7796 (m-80) REVERT: N 1242 PHE cc_start: 0.8519 (t80) cc_final: 0.8309 (t80) REVERT: N 1246 LYS cc_start: 0.8586 (mttt) cc_final: 0.8344 (mttp) REVERT: M 77 VAL cc_start: 0.8424 (t) cc_final: 0.8195 (m) REVERT: M 102 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7581 (mp0) REVERT: M 147 LYS cc_start: 0.8637 (mttt) cc_final: 0.8390 (mttm) REVERT: M 165 MET cc_start: 0.7087 (tpp) cc_final: 0.6851 (tpp) REVERT: M 297 ASN cc_start: 0.7678 (m-40) cc_final: 0.7422 (m-40) REVERT: M 485 ASN cc_start: 0.8169 (t0) cc_final: 0.7346 (t0) REVERT: M 762 LYS cc_start: 0.8022 (mptt) cc_final: 0.7661 (mptt) REVERT: M 766 GLN cc_start: 0.7575 (pp30) cc_final: 0.7050 (pp30) REVERT: M 771 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7851 (mm-30) REVERT: M 795 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7686 (tm-30) REVERT: M 927 SER cc_start: 0.8630 (t) cc_final: 0.8387 (m) REVERT: M 953 GLU cc_start: 0.7049 (mp0) cc_final: 0.6286 (mp0) REVERT: M 1009 ASP cc_start: 0.7814 (m-30) cc_final: 0.7440 (m-30) REVERT: M 1415 GLU cc_start: 0.7945 (tp30) cc_final: 0.7644 (tp30) outliers start: 74 outliers final: 43 residues processed: 649 average time/residue: 0.2002 time to fit residues: 197.2747 Evaluate side-chains 639 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 594 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain N residue 245 GLN Chi-restraints excluded: chain N residue 299 LYS Chi-restraints excluded: chain N residue 306 CYS Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 396 SER Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1007 ILE Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1330 TRP Chi-restraints excluded: chain N residue 1334 LEU Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1370 HIS Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 826 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1391 MET Chi-restraints excluded: chain M residue 1393 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 42 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 318 optimal weight: 0.9990 chunk 282 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 510 ASN D 35 HIS H 87 ASN H 112 HIS N 116 ASN N1370 HIS M1001 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119451 restraints weight = 42288.681| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3179 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29304 Z= 0.220 Angle : 0.578 8.040 40014 Z= 0.303 Chirality : 0.042 0.278 4571 Planarity : 0.005 0.056 5032 Dihedral : 10.345 87.891 4630 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.23 % Allowed : 14.14 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.63 (0.14), residues: 3555 helix: 1.77 (0.12), residues: 1980 sheet: 0.44 (0.29), residues: 320 loop : -1.89 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 90 TYR 0.020 0.002 TYR E 79 PHE 0.028 0.002 PHE I 147 TRP 0.015 0.002 TRP A 134 HIS 0.010 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00532 (29296) covalent geometry : angle 0.57677 (40008) hydrogen bonds : bond 0.05498 ( 1531) hydrogen bonds : angle 3.84482 ( 4455) metal coordination : bond 0.01153 ( 8) metal coordination : angle 2.95114 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 630 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8663 (mmtp) REVERT: A 115 LEU cc_start: 0.8724 (mt) cc_final: 0.8484 (mt) REVERT: A 172 MET cc_start: 0.8604 (mtt) cc_final: 0.8343 (mtp) REVERT: A 245 GLU cc_start: 0.8393 (mp0) cc_final: 0.8057 (mp0) REVERT: A 257 LYS cc_start: 0.8689 (tttm) cc_final: 0.8322 (tttm) REVERT: A 258 PHE cc_start: 0.8000 (t80) cc_final: 0.7510 (t80) REVERT: A 278 LYS cc_start: 0.8632 (mttt) cc_final: 0.8344 (mtmm) REVERT: A 283 ASN cc_start: 0.8627 (t0) cc_final: 0.8394 (t0) REVERT: A 310 GLN cc_start: 0.8373 (tt0) cc_final: 0.7973 (tp-100) REVERT: A 378 GLU cc_start: 0.8138 (tt0) cc_final: 0.7835 (tt0) REVERT: A 383 MET cc_start: 0.8614 (mmm) cc_final: 0.8296 (tpp) REVERT: A 447 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 647 ARG cc_start: 0.8573 (ptm160) cc_final: 0.8166 (ttt180) REVERT: A 722 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 756 ILE cc_start: 0.8866 (mt) cc_final: 0.8650 (mm) REVERT: A 850 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7947 (tm-30) REVERT: D 31 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (p) REVERT: D 34 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8313 (mm-30) REVERT: H 60 ASN cc_start: 0.8581 (m-40) cc_final: 0.8118 (m110) REVERT: H 148 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.6845 (mmt90) REVERT: I 38 LYS cc_start: 0.8158 (tttt) cc_final: 0.7883 (tttt) REVERT: I 39 ASN cc_start: 0.6902 (m-40) cc_final: 0.6610 (m-40) REVERT: I 66 LEU cc_start: 0.7928 (mt) cc_final: 0.7696 (tp) REVERT: I 168 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3725 (tpp) REVERT: N 318 SER cc_start: 0.8452 (m) cc_final: 0.8117 (p) REVERT: N 453 LEU cc_start: 0.8608 (mt) cc_final: 0.8399 (mp) REVERT: N 898 GLU cc_start: 0.7935 (mp0) cc_final: 0.7322 (mp0) REVERT: N 930 PHE cc_start: 0.8560 (t80) cc_final: 0.8340 (t80) REVERT: N 931 ASP cc_start: 0.7873 (t0) cc_final: 0.7478 (t0) REVERT: N 958 GLU cc_start: 0.7586 (tp30) cc_final: 0.6977 (tp30) REVERT: N 1241 TYR cc_start: 0.8389 (m-80) cc_final: 0.7857 (m-80) REVERT: N 1303 THR cc_start: 0.8925 (p) cc_final: 0.8682 (m) REVERT: N 1338 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: N 1354 MET cc_start: 0.7622 (ttt) cc_final: 0.7395 (ttt) REVERT: M 102 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7628 (mp0) REVERT: M 147 LYS cc_start: 0.8644 (mttt) cc_final: 0.8404 (mttm) REVERT: M 165 MET cc_start: 0.7074 (tpp) cc_final: 0.6826 (tpp) REVERT: M 297 ASN cc_start: 0.7704 (m-40) cc_final: 0.7434 (m-40) REVERT: M 485 ASN cc_start: 0.8152 (t0) cc_final: 0.7728 (t0) REVERT: M 762 LYS cc_start: 0.8053 (mptt) cc_final: 0.7676 (mptt) REVERT: M 771 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7836 (mm-30) REVERT: M 795 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7746 (tm-30) REVERT: M 796 LEU cc_start: 0.8730 (mt) cc_final: 0.8250 (mt) REVERT: M 908 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7950 (tm-30) REVERT: M 927 SER cc_start: 0.8704 (t) cc_final: 0.8441 (m) REVERT: M 1009 ASP cc_start: 0.7833 (m-30) cc_final: 0.7457 (m-30) REVERT: M 1307 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7573 (m90) REVERT: M 1378 GLN cc_start: 0.7469 (tp40) cc_final: 0.6969 (tp40) REVERT: M 1379 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7267 (mmm160) REVERT: M 1391 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8053 (tpp) REVERT: M 1415 GLU cc_start: 0.7976 (tp30) cc_final: 0.7162 (tp30) REVERT: M 1418 HIS cc_start: 0.8038 (m170) cc_final: 0.7803 (m-70) outliers start: 91 outliers final: 55 residues processed: 672 average time/residue: 0.1945 time to fit residues: 199.8474 Evaluate side-chains 679 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 618 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 446 THR Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1007 ILE Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1370 HIS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 826 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1013 ASP Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1379 ARG Chi-restraints excluded: chain M residue 1391 MET Chi-restraints excluded: chain M residue 1393 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 221 optimal weight: 1.9990 chunk 320 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 333 optimal weight: 0.6980 chunk 276 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 327 optimal weight: 0.6980 chunk 149 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 699 GLN C 42 GLN D 35 HIS H 49 ASN H 84 HIS N 116 ASN N 155 HIS N1370 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120333 restraints weight = 42240.935| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.07 r_work: 0.3188 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29304 Z= 0.175 Angle : 0.545 6.780 40014 Z= 0.287 Chirality : 0.041 0.261 4571 Planarity : 0.005 0.054 5032 Dihedral : 10.341 88.511 4628 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.95 % Allowed : 15.25 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.67 (0.14), residues: 3555 helix: 1.85 (0.12), residues: 1978 sheet: 0.25 (0.28), residues: 326 loop : -1.91 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 773 TYR 0.017 0.001 TYR E 79 PHE 0.027 0.002 PHE I 147 TRP 0.023 0.001 TRP N1330 HIS 0.013 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00418 (29296) covalent geometry : angle 0.54471 (40008) hydrogen bonds : bond 0.04878 ( 1531) hydrogen bonds : angle 3.74814 ( 4455) metal coordination : bond 0.00849 ( 8) metal coordination : angle 1.98828 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 623 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8730 (mt) cc_final: 0.8437 (mt) REVERT: A 172 MET cc_start: 0.8566 (mtt) cc_final: 0.8296 (mtp) REVERT: A 245 GLU cc_start: 0.8366 (mp0) cc_final: 0.8063 (mp0) REVERT: A 257 LYS cc_start: 0.8720 (tttm) cc_final: 0.8373 (tttm) REVERT: A 258 PHE cc_start: 0.8035 (t80) cc_final: 0.7151 (t80) REVERT: A 278 LYS cc_start: 0.8632 (mttt) cc_final: 0.8338 (mtmm) REVERT: A 283 ASN cc_start: 0.8581 (t0) cc_final: 0.8362 (t0) REVERT: A 310 GLN cc_start: 0.8349 (tt0) cc_final: 0.8094 (tp-100) REVERT: A 395 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: A 447 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 756 ILE cc_start: 0.8881 (mt) cc_final: 0.8662 (mm) REVERT: A 850 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 75 MET cc_start: 0.8187 (mtm) cc_final: 0.7850 (mtm) REVERT: D 102 GLU cc_start: 0.8263 (mp0) cc_final: 0.7861 (mp0) REVERT: E 45 MET cc_start: 0.7964 (ttm) cc_final: 0.7757 (ttm) REVERT: H 60 ASN cc_start: 0.8573 (m-40) cc_final: 0.8306 (m-40) REVERT: I 38 LYS cc_start: 0.8199 (tttt) cc_final: 0.7952 (tttt) REVERT: I 39 ASN cc_start: 0.6916 (m-40) cc_final: 0.6628 (m-40) REVERT: I 168 MET cc_start: 0.4232 (OUTLIER) cc_final: 0.3930 (tpp) REVERT: N 318 SER cc_start: 0.8462 (m) cc_final: 0.8132 (p) REVERT: N 372 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8281 (tt) REVERT: N 453 LEU cc_start: 0.8613 (mt) cc_final: 0.8395 (mp) REVERT: N 799 ASP cc_start: 0.8254 (t70) cc_final: 0.7985 (t0) REVERT: N 898 GLU cc_start: 0.7939 (mp0) cc_final: 0.7351 (mp0) REVERT: N 903 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8653 (mtt-85) REVERT: N 931 ASP cc_start: 0.7916 (t0) cc_final: 0.7510 (t0) REVERT: N 958 GLU cc_start: 0.7614 (tp30) cc_final: 0.7024 (tp30) REVERT: N 1241 TYR cc_start: 0.8371 (m-80) cc_final: 0.7786 (m-80) REVERT: N 1338 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: N 1354 MET cc_start: 0.7628 (ttt) cc_final: 0.7382 (ttt) REVERT: N 1360 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: M 102 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7615 (mp0) REVERT: M 147 LYS cc_start: 0.8657 (mttt) cc_final: 0.8350 (mttm) REVERT: M 165 MET cc_start: 0.6998 (tpp) cc_final: 0.6783 (tpp) REVERT: M 297 ASN cc_start: 0.7697 (m-40) cc_final: 0.7433 (m-40) REVERT: M 485 ASN cc_start: 0.8154 (t0) cc_final: 0.7730 (t0) REVERT: M 762 LYS cc_start: 0.8056 (mptt) cc_final: 0.7732 (mptt) REVERT: M 766 GLN cc_start: 0.7589 (pp30) cc_final: 0.7029 (pp30) REVERT: M 771 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7840 (mm-30) REVERT: M 795 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7730 (tm-30) REVERT: M 796 LEU cc_start: 0.8731 (mt) cc_final: 0.8270 (mt) REVERT: M 807 LEU cc_start: 0.7621 (mt) cc_final: 0.7399 (mt) REVERT: M 908 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7993 (tm-30) REVERT: M 911 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: M 927 SER cc_start: 0.8714 (t) cc_final: 0.8441 (m) REVERT: M 1000 ASP cc_start: 0.7908 (t0) cc_final: 0.7608 (t0) REVERT: M 1009 ASP cc_start: 0.7847 (m-30) cc_final: 0.7453 (m-30) REVERT: M 1307 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7549 (m90) REVERT: M 1351 ASP cc_start: 0.7609 (t70) cc_final: 0.7318 (t70) REVERT: M 1378 GLN cc_start: 0.7522 (tp40) cc_final: 0.7004 (tp40) REVERT: M 1379 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7108 (mmm160) REVERT: M 1415 GLU cc_start: 0.8003 (tp30) cc_final: 0.7217 (tp30) outliers start: 83 outliers final: 57 residues processed: 663 average time/residue: 0.1975 time to fit residues: 199.9066 Evaluate side-chains 677 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 613 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 446 THR Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1370 HIS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 799 ASP Chi-restraints excluded: chain M residue 826 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 911 GLU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1013 ASP Chi-restraints excluded: chain M residue 1250 ILE Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1379 ARG Chi-restraints excluded: chain M residue 1393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 chunk 259 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 209 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 510 ASN A 699 GLN D 35 HIS H 87 ASN N 116 ASN N 975 HIS N1307 HIS N1370 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119938 restraints weight = 42133.603| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.06 r_work: 0.3184 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29304 Z= 0.181 Angle : 0.550 8.053 40014 Z= 0.290 Chirality : 0.041 0.263 4571 Planarity : 0.005 0.053 5032 Dihedral : 10.305 88.529 4624 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.23 % Allowed : 15.64 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.14), residues: 3555 helix: 1.90 (0.12), residues: 1972 sheet: 0.24 (0.29), residues: 324 loop : -1.89 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 370 TYR 0.017 0.001 TYR N 123 PHE 0.025 0.002 PHE I 147 TRP 0.014 0.001 TRP A 134 HIS 0.007 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00434 (29296) covalent geometry : angle 0.54940 (40008) hydrogen bonds : bond 0.04932 ( 1531) hydrogen bonds : angle 3.72674 ( 4455) metal coordination : bond 0.00998 ( 8) metal coordination : angle 2.00765 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 629 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.8445 (p) cc_final: 0.8240 (m) REVERT: A 62 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8675 (mmtp) REVERT: A 172 MET cc_start: 0.8588 (mtt) cc_final: 0.8319 (mtp) REVERT: A 245 GLU cc_start: 0.8354 (mp0) cc_final: 0.7940 (mp0) REVERT: A 257 LYS cc_start: 0.8735 (tttm) cc_final: 0.8407 (tttm) REVERT: A 258 PHE cc_start: 0.8052 (t80) cc_final: 0.7441 (t80) REVERT: A 278 LYS cc_start: 0.8598 (mttt) cc_final: 0.8301 (mtmm) REVERT: A 283 ASN cc_start: 0.8572 (t0) cc_final: 0.8345 (t0) REVERT: A 310 GLN cc_start: 0.8404 (tt0) cc_final: 0.8087 (tp-100) REVERT: A 395 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: A 447 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 623 ASN cc_start: 0.8242 (t0) cc_final: 0.8012 (t0) REVERT: A 689 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 756 ILE cc_start: 0.8875 (mt) cc_final: 0.8657 (mm) REVERT: A 850 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 851 ASP cc_start: 0.8296 (m-30) cc_final: 0.7921 (m-30) REVERT: D 17 MET cc_start: 0.7673 (mmm) cc_final: 0.7352 (tmm) REVERT: D 102 GLU cc_start: 0.8266 (mp0) cc_final: 0.7970 (mp0) REVERT: E 45 MET cc_start: 0.8043 (ttm) cc_final: 0.7790 (ttm) REVERT: H 60 ASN cc_start: 0.8639 (m-40) cc_final: 0.8194 (m110) REVERT: H 118 MET cc_start: 0.7595 (mmm) cc_final: 0.7290 (mmt) REVERT: I 38 LYS cc_start: 0.8201 (tttt) cc_final: 0.7946 (tttt) REVERT: I 39 ASN cc_start: 0.6945 (m-40) cc_final: 0.6652 (m-40) REVERT: I 168 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3960 (tpp) REVERT: N 318 SER cc_start: 0.8461 (m) cc_final: 0.8135 (p) REVERT: N 372 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8285 (tt) REVERT: N 453 LEU cc_start: 0.8594 (mt) cc_final: 0.8377 (mp) REVERT: N 799 ASP cc_start: 0.8264 (t70) cc_final: 0.7987 (t0) REVERT: N 898 GLU cc_start: 0.7925 (mp0) cc_final: 0.7353 (mp0) REVERT: N 903 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8592 (mtt-85) REVERT: N 931 ASP cc_start: 0.7895 (t0) cc_final: 0.7524 (t0) REVERT: N 1241 TYR cc_start: 0.8400 (m-80) cc_final: 0.7802 (m-80) REVERT: N 1246 LYS cc_start: 0.8630 (mttt) cc_final: 0.8323 (mttm) REVERT: N 1338 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: N 1354 MET cc_start: 0.7635 (ttt) cc_final: 0.7394 (ttt) REVERT: N 1360 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: M 165 MET cc_start: 0.7100 (tpp) cc_final: 0.6826 (tpp) REVERT: M 297 ASN cc_start: 0.7709 (m-40) cc_final: 0.7439 (m-40) REVERT: M 485 ASN cc_start: 0.8164 (t0) cc_final: 0.7724 (t0) REVERT: M 762 LYS cc_start: 0.8077 (mptt) cc_final: 0.7760 (mptt) REVERT: M 766 GLN cc_start: 0.7590 (pp30) cc_final: 0.7037 (pp30) REVERT: M 771 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7826 (mm-30) REVERT: M 795 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7732 (tm-30) REVERT: M 796 LEU cc_start: 0.8721 (mt) cc_final: 0.8230 (mt) REVERT: M 907 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7847 (mm-30) REVERT: M 908 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7857 (tm-30) REVERT: M 911 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7498 (pp20) REVERT: M 927 SER cc_start: 0.8748 (t) cc_final: 0.8468 (m) REVERT: M 1009 ASP cc_start: 0.7879 (m-30) cc_final: 0.7472 (m-30) REVERT: M 1307 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7541 (m90) REVERT: M 1351 ASP cc_start: 0.7667 (t70) cc_final: 0.7344 (t70) REVERT: M 1378 GLN cc_start: 0.7512 (tp40) cc_final: 0.7005 (tp40) REVERT: M 1379 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7101 (mmm160) REVERT: M 1391 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8079 (tpp) REVERT: M 1415 GLU cc_start: 0.8011 (tp30) cc_final: 0.7252 (tp30) outliers start: 91 outliers final: 67 residues processed: 673 average time/residue: 0.1931 time to fit residues: 199.3784 Evaluate side-chains 690 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 616 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 968 THR Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 971 SER Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1295 VAL Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1326 LEU Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1370 HIS Chi-restraints excluded: chain N residue 1404 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 799 ASP Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1379 ARG Chi-restraints excluded: chain M residue 1391 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 112 optimal weight: 0.3980 chunk 181 optimal weight: 0.0050 chunk 237 optimal weight: 0.8980 chunk 205 optimal weight: 0.0670 chunk 238 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 325 optimal weight: 0.9990 chunk 152 optimal weight: 0.0670 overall best weight: 0.2670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 510 ASN A 699 GLN D 35 HIS N 116 ASN N1307 HIS N1370 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121759 restraints weight = 42229.190| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.06 r_work: 0.3220 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29304 Z= 0.114 Angle : 0.512 10.214 40014 Z= 0.268 Chirality : 0.039 0.214 4571 Planarity : 0.005 0.051 5032 Dihedral : 10.266 88.009 4624 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.02 % Allowed : 16.56 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.89 (0.15), residues: 3555 helix: 2.06 (0.12), residues: 1974 sheet: 0.25 (0.28), residues: 331 loop : -1.83 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 773 TYR 0.014 0.001 TYR N 123 PHE 0.023 0.001 PHE I 147 TRP 0.013 0.001 TRP M1420 HIS 0.015 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00257 (29296) covalent geometry : angle 0.51192 (40008) hydrogen bonds : bond 0.03823 ( 1531) hydrogen bonds : angle 3.60477 ( 4455) metal coordination : bond 0.00266 ( 8) metal coordination : angle 1.32632 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 623 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8558 (mtt) cc_final: 0.8297 (mtp) REVERT: A 245 GLU cc_start: 0.8334 (mp0) cc_final: 0.7925 (mp0) REVERT: A 257 LYS cc_start: 0.8734 (tttm) cc_final: 0.8468 (tttm) REVERT: A 258 PHE cc_start: 0.8004 (t80) cc_final: 0.7378 (t80) REVERT: A 278 LYS cc_start: 0.8571 (mttt) cc_final: 0.8303 (mtmm) REVERT: A 283 ASN cc_start: 0.8529 (t0) cc_final: 0.8305 (t0) REVERT: A 298 GLN cc_start: 0.8439 (mt0) cc_final: 0.8104 (mp10) REVERT: A 310 GLN cc_start: 0.8378 (tt0) cc_final: 0.8052 (tp-100) REVERT: A 395 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: A 447 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 689 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 756 ILE cc_start: 0.8876 (mt) cc_final: 0.8655 (mm) REVERT: A 850 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 851 ASP cc_start: 0.8289 (m-30) cc_final: 0.7898 (m-30) REVERT: D 17 MET cc_start: 0.7674 (mmm) cc_final: 0.7307 (tmm) REVERT: D 75 MET cc_start: 0.8198 (mtm) cc_final: 0.7895 (mtm) REVERT: D 102 GLU cc_start: 0.8273 (mp0) cc_final: 0.7871 (mp0) REVERT: H 60 ASN cc_start: 0.8641 (m-40) cc_final: 0.8156 (m110) REVERT: H 118 MET cc_start: 0.7584 (mmm) cc_final: 0.7298 (mmt) REVERT: I 38 LYS cc_start: 0.8150 (tttt) cc_final: 0.7912 (tttt) REVERT: I 39 ASN cc_start: 0.6966 (m-40) cc_final: 0.6675 (m-40) REVERT: N 318 SER cc_start: 0.8504 (m) cc_final: 0.8181 (p) REVERT: N 359 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8141 (ttmm) REVERT: N 372 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8234 (tt) REVERT: N 799 ASP cc_start: 0.8228 (t70) cc_final: 0.7944 (t0) REVERT: N 898 GLU cc_start: 0.7833 (mp0) cc_final: 0.7307 (mp0) REVERT: N 903 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8589 (mtt-85) REVERT: N 930 PHE cc_start: 0.8567 (t80) cc_final: 0.8348 (t80) REVERT: N 931 ASP cc_start: 0.7865 (t0) cc_final: 0.7439 (t0) REVERT: N 1241 TYR cc_start: 0.8345 (m-80) cc_final: 0.7753 (m-80) REVERT: N 1338 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: N 1354 MET cc_start: 0.7564 (ttt) cc_final: 0.7333 (ttt) REVERT: N 1360 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: M 116 ASN cc_start: 0.7982 (p0) cc_final: 0.7781 (p0) REVERT: M 165 MET cc_start: 0.7073 (tpp) cc_final: 0.6794 (tpp) REVERT: M 297 ASN cc_start: 0.7691 (m-40) cc_final: 0.7430 (m-40) REVERT: M 345 GLU cc_start: 0.7582 (tt0) cc_final: 0.6680 (tm-30) REVERT: M 485 ASN cc_start: 0.8167 (t0) cc_final: 0.7763 (t0) REVERT: M 762 LYS cc_start: 0.8090 (mptt) cc_final: 0.7776 (mptt) REVERT: M 766 GLN cc_start: 0.7577 (pp30) cc_final: 0.7056 (pp30) REVERT: M 771 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7809 (mm-30) REVERT: M 795 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7686 (tm-30) REVERT: M 796 LEU cc_start: 0.8729 (mt) cc_final: 0.8283 (mt) REVERT: M 908 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7893 (tm-30) REVERT: M 911 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7443 (pp20) REVERT: M 927 SER cc_start: 0.8725 (t) cc_final: 0.8430 (m) REVERT: M 1009 ASP cc_start: 0.7890 (m-30) cc_final: 0.7476 (m-30) REVERT: M 1307 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7657 (m90) REVERT: M 1378 GLN cc_start: 0.7552 (tp40) cc_final: 0.7019 (tp40) REVERT: M 1415 GLU cc_start: 0.8018 (tp30) cc_final: 0.7282 (tp30) outliers start: 85 outliers final: 52 residues processed: 666 average time/residue: 0.1927 time to fit residues: 197.1174 Evaluate side-chains 665 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 609 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 74 TYR Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 968 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1295 VAL Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1404 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 995 ILE Chi-restraints excluded: chain M residue 1250 ILE Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1328 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 168 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 187 optimal weight: 0.1980 chunk 199 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 699 GLN D 35 HIS N 116 ASN ** N 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1307 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119660 restraints weight = 42262.517| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.07 r_work: 0.3187 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29304 Z= 0.192 Angle : 0.565 8.553 40014 Z= 0.295 Chirality : 0.041 0.265 4571 Planarity : 0.005 0.052 5032 Dihedral : 10.250 87.592 4624 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.84 % Allowed : 16.99 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.81 (0.14), residues: 3555 helix: 1.99 (0.12), residues: 1974 sheet: 0.22 (0.28), residues: 326 loop : -1.86 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 321 TYR 0.017 0.001 TYR N 123 PHE 0.022 0.002 PHE I 147 TRP 0.014 0.002 TRP M 486 HIS 0.008 0.001 HIS N1370 Details of bonding type rmsd covalent geometry : bond 0.00465 (29296) covalent geometry : angle 0.56405 (40008) hydrogen bonds : bond 0.05005 ( 1531) hydrogen bonds : angle 3.71020 ( 4455) metal coordination : bond 0.01238 ( 8) metal coordination : angle 2.02610 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 617 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8591 (mtt) cc_final: 0.8324 (mtp) REVERT: A 245 GLU cc_start: 0.8354 (mp0) cc_final: 0.8054 (mp0) REVERT: A 257 LYS cc_start: 0.8732 (tttm) cc_final: 0.8463 (tttm) REVERT: A 258 PHE cc_start: 0.8108 (t80) cc_final: 0.7562 (t80) REVERT: A 278 LYS cc_start: 0.8552 (mttt) cc_final: 0.8280 (mtmm) REVERT: A 283 ASN cc_start: 0.8576 (t0) cc_final: 0.8348 (t0) REVERT: A 298 GLN cc_start: 0.8517 (mt0) cc_final: 0.8169 (mp10) REVERT: A 310 GLN cc_start: 0.8387 (tt0) cc_final: 0.8060 (tp-100) REVERT: A 395 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7977 (mtm-85) REVERT: A 447 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 623 ASN cc_start: 0.8210 (t0) cc_final: 0.7979 (t0) REVERT: A 689 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 756 ILE cc_start: 0.8861 (mt) cc_final: 0.8650 (mm) REVERT: A 850 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 851 ASP cc_start: 0.8331 (m-30) cc_final: 0.7930 (m-30) REVERT: D 17 MET cc_start: 0.7654 (mmm) cc_final: 0.7279 (tmm) REVERT: D 75 MET cc_start: 0.8210 (mtm) cc_final: 0.7867 (mtm) REVERT: H 17 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (ttt-90) REVERT: H 60 ASN cc_start: 0.8645 (m-40) cc_final: 0.8401 (m-40) REVERT: H 118 MET cc_start: 0.7566 (mmm) cc_final: 0.7254 (mmt) REVERT: I 38 LYS cc_start: 0.8166 (tttt) cc_final: 0.7922 (tttt) REVERT: I 39 ASN cc_start: 0.6972 (m-40) cc_final: 0.6681 (m-40) REVERT: N 318 SER cc_start: 0.8481 (m) cc_final: 0.8153 (p) REVERT: N 372 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8291 (tt) REVERT: N 453 LEU cc_start: 0.8591 (mt) cc_final: 0.8390 (mp) REVERT: N 799 ASP cc_start: 0.8258 (t70) cc_final: 0.7978 (t0) REVERT: N 898 GLU cc_start: 0.7875 (mp0) cc_final: 0.7327 (mp0) REVERT: N 903 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8610 (mtt-85) REVERT: N 931 ASP cc_start: 0.7885 (t0) cc_final: 0.7454 (t0) REVERT: N 1241 TYR cc_start: 0.8407 (m-80) cc_final: 0.7776 (m-80) REVERT: N 1338 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: N 1354 MET cc_start: 0.7581 (ttt) cc_final: 0.7292 (ttt) REVERT: N 1360 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: M 165 MET cc_start: 0.6974 (tpp) cc_final: 0.6729 (tpp) REVERT: M 297 ASN cc_start: 0.7707 (m-40) cc_final: 0.7426 (m-40) REVERT: M 345 GLU cc_start: 0.7657 (tt0) cc_final: 0.6773 (tm-30) REVERT: M 485 ASN cc_start: 0.8193 (t0) cc_final: 0.7801 (t0) REVERT: M 762 LYS cc_start: 0.8089 (mptt) cc_final: 0.7792 (mptt) REVERT: M 766 GLN cc_start: 0.7621 (pp30) cc_final: 0.7076 (pp30) REVERT: M 771 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7805 (mm-30) REVERT: M 795 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7701 (tm-30) REVERT: M 796 LEU cc_start: 0.8704 (mt) cc_final: 0.8224 (mt) REVERT: M 907 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7885 (mm-30) REVERT: M 908 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7961 (tm-30) REVERT: M 911 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7468 (pp20) REVERT: M 927 SER cc_start: 0.8764 (t) cc_final: 0.8484 (m) REVERT: M 966 MET cc_start: 0.8581 (mtt) cc_final: 0.8214 (mtp) REVERT: M 1009 ASP cc_start: 0.7898 (m-30) cc_final: 0.7501 (m-30) REVERT: M 1307 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7582 (m90) REVERT: M 1378 GLN cc_start: 0.7516 (tp40) cc_final: 0.7078 (tp40) REVERT: M 1415 GLU cc_start: 0.8024 (tp30) cc_final: 0.7495 (tp30) REVERT: M 1424 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6629 (p90) outliers start: 80 outliers final: 61 residues processed: 656 average time/residue: 0.2053 time to fit residues: 204.6600 Evaluate side-chains 684 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 617 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 968 THR Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1295 VAL Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1404 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 826 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1328 GLU Chi-restraints excluded: chain M residue 1424 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 324 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 265 optimal weight: 0.0570 chunk 322 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 699 GLN D 35 HIS N 116 ASN ** N 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1307 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120832 restraints weight = 42145.684| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.07 r_work: 0.3205 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29304 Z= 0.136 Angle : 0.537 8.815 40014 Z= 0.280 Chirality : 0.039 0.228 4571 Planarity : 0.005 0.051 5032 Dihedral : 10.252 87.871 4624 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.63 % Allowed : 17.34 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.91 (0.14), residues: 3555 helix: 2.09 (0.12), residues: 1978 sheet: 0.25 (0.28), residues: 331 loop : -1.85 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 773 TYR 0.016 0.001 TYR N 123 PHE 0.023 0.001 PHE I 147 TRP 0.011 0.001 TRP A 451 HIS 0.006 0.001 HIS M 851 Details of bonding type rmsd covalent geometry : bond 0.00318 (29296) covalent geometry : angle 0.53671 (40008) hydrogen bonds : bond 0.04223 ( 1531) hydrogen bonds : angle 3.62395 ( 4455) metal coordination : bond 0.00530 ( 8) metal coordination : angle 1.51478 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 616 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8567 (mtt) cc_final: 0.8305 (mtp) REVERT: A 245 GLU cc_start: 0.8347 (mp0) cc_final: 0.7929 (mp0) REVERT: A 257 LYS cc_start: 0.8737 (tttm) cc_final: 0.8459 (tttm) REVERT: A 258 PHE cc_start: 0.8045 (t80) cc_final: 0.7497 (t80) REVERT: A 278 LYS cc_start: 0.8543 (mttt) cc_final: 0.8276 (mtmm) REVERT: A 283 ASN cc_start: 0.8539 (t0) cc_final: 0.8312 (t0) REVERT: A 298 GLN cc_start: 0.8495 (mt0) cc_final: 0.8187 (mm-40) REVERT: A 310 GLN cc_start: 0.8372 (tt0) cc_final: 0.8040 (tp-100) REVERT: A 395 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: A 447 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 689 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 756 ILE cc_start: 0.8876 (mt) cc_final: 0.8659 (mm) REVERT: A 850 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 851 ASP cc_start: 0.8333 (m-30) cc_final: 0.7945 (m-30) REVERT: D 17 MET cc_start: 0.7642 (mmm) cc_final: 0.7245 (tmm) REVERT: D 75 MET cc_start: 0.8207 (mtm) cc_final: 0.7936 (mtm) REVERT: E 45 MET cc_start: 0.8200 (ttm) cc_final: 0.7931 (ttm) REVERT: H 60 ASN cc_start: 0.8642 (m-40) cc_final: 0.8183 (m110) REVERT: H 118 MET cc_start: 0.7567 (mmm) cc_final: 0.7270 (mmt) REVERT: I 38 LYS cc_start: 0.8158 (tttt) cc_final: 0.7904 (tttt) REVERT: I 39 ASN cc_start: 0.6917 (m-40) cc_final: 0.6648 (m-40) REVERT: I 52 LEU cc_start: 0.6518 (mp) cc_final: 0.6295 (mt) REVERT: I 64 MET cc_start: 0.8188 (mmm) cc_final: 0.7831 (tmm) REVERT: N 318 SER cc_start: 0.8521 (m) cc_final: 0.8203 (p) REVERT: N 372 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8256 (tt) REVERT: N 453 LEU cc_start: 0.8559 (mt) cc_final: 0.8348 (mp) REVERT: N 799 ASP cc_start: 0.8258 (t70) cc_final: 0.7970 (t0) REVERT: N 898 GLU cc_start: 0.7811 (mp0) cc_final: 0.7280 (mp0) REVERT: N 903 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8604 (mtt-85) REVERT: N 931 ASP cc_start: 0.7884 (t0) cc_final: 0.7472 (t0) REVERT: N 1241 TYR cc_start: 0.8371 (m-80) cc_final: 0.7749 (m-80) REVERT: N 1338 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: N 1354 MET cc_start: 0.7607 (ttt) cc_final: 0.7298 (ttt) REVERT: N 1360 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: M 165 MET cc_start: 0.6972 (tpp) cc_final: 0.6696 (tpp) REVERT: M 297 ASN cc_start: 0.7685 (m-40) cc_final: 0.7408 (m-40) REVERT: M 345 GLU cc_start: 0.7607 (tt0) cc_final: 0.6718 (tm-30) REVERT: M 485 ASN cc_start: 0.8194 (t0) cc_final: 0.7806 (t0) REVERT: M 762 LYS cc_start: 0.8090 (mptt) cc_final: 0.7785 (mptt) REVERT: M 766 GLN cc_start: 0.7558 (pp30) cc_final: 0.7064 (pp30) REVERT: M 771 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7794 (mm-30) REVERT: M 795 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7679 (tm-30) REVERT: M 796 LEU cc_start: 0.8693 (mt) cc_final: 0.8221 (mt) REVERT: M 907 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7836 (mm-30) REVERT: M 908 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7847 (tm-30) REVERT: M 911 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7428 (pp20) REVERT: M 927 SER cc_start: 0.8731 (t) cc_final: 0.8439 (m) REVERT: M 966 MET cc_start: 0.8566 (mtt) cc_final: 0.8262 (mtp) REVERT: M 1009 ASP cc_start: 0.7900 (m-30) cc_final: 0.7495 (m-30) REVERT: M 1307 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7616 (m90) REVERT: M 1378 GLN cc_start: 0.7513 (tp40) cc_final: 0.7083 (tp40) REVERT: M 1385 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7731 (ttmt) REVERT: M 1415 GLU cc_start: 0.8030 (tp30) cc_final: 0.7504 (tp30) REVERT: M 1424 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6600 (p90) outliers start: 74 outliers final: 61 residues processed: 652 average time/residue: 0.1965 time to fit residues: 196.6695 Evaluate side-chains 681 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 615 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 446 THR Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 968 THR Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1295 VAL Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1404 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 445 CYS Chi-restraints excluded: chain M residue 807 LEU Chi-restraints excluded: chain M residue 826 GLN Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1328 GLU Chi-restraints excluded: chain M residue 1424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 156 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 346 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 336 HIS A 510 ASN A 699 GLN D 35 HIS E 27 HIS I 95 ASN I 113 GLN N 116 ASN ** N1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1307 HIS N1657 ASN M 798 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119582 restraints weight = 41717.314| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.41 r_work: 0.3129 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 29304 Z= 0.369 Angle : 0.713 9.803 40014 Z= 0.370 Chirality : 0.049 0.321 4571 Planarity : 0.006 0.060 5032 Dihedral : 10.403 89.297 4624 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.63 % Allowed : 17.41 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3555 helix: 1.63 (0.12), residues: 1976 sheet: 0.18 (0.29), residues: 322 loop : -2.02 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 773 TYR 0.029 0.002 TYR I 125 PHE 0.029 0.003 PHE A 811 TRP 0.021 0.003 TRP N 196 HIS 0.013 0.002 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00896 (29296) covalent geometry : angle 0.71207 (40008) hydrogen bonds : bond 0.07092 ( 1531) hydrogen bonds : angle 4.00621 ( 4455) metal coordination : bond 0.02542 ( 8) metal coordination : angle 3.14106 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 629 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8713 (mtt) cc_final: 0.8450 (mtp) REVERT: A 245 GLU cc_start: 0.8399 (mp0) cc_final: 0.8033 (mp0) REVERT: A 258 PHE cc_start: 0.8271 (t80) cc_final: 0.7757 (t80) REVERT: A 278 LYS cc_start: 0.8600 (mttt) cc_final: 0.8345 (mtmm) REVERT: A 283 ASN cc_start: 0.8655 (t0) cc_final: 0.8429 (t0) REVERT: A 298 GLN cc_start: 0.8615 (mt0) cc_final: 0.8262 (mp10) REVERT: A 310 GLN cc_start: 0.8398 (tt0) cc_final: 0.8099 (tp-100) REVERT: A 403 ASP cc_start: 0.8235 (m-30) cc_final: 0.7986 (t0) REVERT: A 850 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 851 ASP cc_start: 0.8342 (m-30) cc_final: 0.8079 (m-30) REVERT: D 17 MET cc_start: 0.7653 (mmm) cc_final: 0.7313 (tmm) REVERT: E 45 MET cc_start: 0.8480 (ttm) cc_final: 0.8268 (ttm) REVERT: H 17 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (ttt-90) REVERT: H 60 ASN cc_start: 0.8696 (m-40) cc_final: 0.8460 (m-40) REVERT: H 90 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7538 (ttm-80) REVERT: H 118 MET cc_start: 0.7633 (mmm) cc_final: 0.7300 (mmt) REVERT: I 38 LYS cc_start: 0.8178 (tttt) cc_final: 0.7961 (tttt) REVERT: I 39 ASN cc_start: 0.7091 (m-40) cc_final: 0.6806 (m-40) REVERT: I 59 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7846 (mtp85) REVERT: I 126 MET cc_start: 0.8466 (mmm) cc_final: 0.8187 (tpp) REVERT: I 144 LEU cc_start: 0.7764 (mt) cc_final: 0.7466 (mm) REVERT: N 187 SER cc_start: 0.8827 (t) cc_final: 0.8405 (m) REVERT: N 318 SER cc_start: 0.8534 (m) cc_final: 0.8200 (p) REVERT: N 453 LEU cc_start: 0.8690 (mt) cc_final: 0.8484 (mp) REVERT: N 898 GLU cc_start: 0.7919 (mp0) cc_final: 0.7324 (mp0) REVERT: N 903 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8732 (mtt-85) REVERT: N 931 ASP cc_start: 0.7976 (t0) cc_final: 0.7584 (t0) REVERT: N 934 CYS cc_start: 0.8167 (t) cc_final: 0.7770 (t) REVERT: N 1338 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: N 1354 MET cc_start: 0.7692 (ttt) cc_final: 0.7351 (ttt) REVERT: N 1360 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: N 1370 HIS cc_start: 0.8163 (p-80) cc_final: 0.7607 (p-80) REVERT: M 139 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8053 (tm-30) REVERT: M 143 MET cc_start: 0.6941 (mtp) cc_final: 0.6728 (ptm) REVERT: M 165 MET cc_start: 0.7052 (tpp) cc_final: 0.6796 (tpp) REVERT: M 297 ASN cc_start: 0.7785 (m-40) cc_final: 0.7493 (m-40) REVERT: M 299 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7152 (mtmt) REVERT: M 345 GLU cc_start: 0.7811 (tt0) cc_final: 0.7025 (tm-30) REVERT: M 455 VAL cc_start: 0.8247 (p) cc_final: 0.8047 (p) REVERT: M 485 ASN cc_start: 0.8236 (t0) cc_final: 0.7881 (t0) REVERT: M 762 LYS cc_start: 0.8079 (mptt) cc_final: 0.7815 (mptt) REVERT: M 766 GLN cc_start: 0.7733 (pp30) cc_final: 0.7195 (pp30) REVERT: M 771 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7940 (mm-30) REVERT: M 795 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7717 (tm-30) REVERT: M 796 LEU cc_start: 0.8738 (mt) cc_final: 0.8259 (mt) REVERT: M 808 LYS cc_start: 0.8687 (tttt) cc_final: 0.8315 (tttt) REVERT: M 907 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8032 (mm-30) REVERT: M 908 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7822 (tm-30) REVERT: M 911 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7495 (pp20) REVERT: M 927 SER cc_start: 0.8819 (t) cc_final: 0.8545 (m) REVERT: M 966 MET cc_start: 0.8612 (mtt) cc_final: 0.8251 (mtp) REVERT: M 1009 ASP cc_start: 0.7938 (m-30) cc_final: 0.7570 (m-30) REVERT: M 1307 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.7524 (m90) REVERT: M 1324 THR cc_start: 0.8707 (t) cc_final: 0.8503 (m) REVERT: M 1378 GLN cc_start: 0.7590 (tp40) cc_final: 0.7102 (tp40) REVERT: M 1415 GLU cc_start: 0.8030 (tp30) cc_final: 0.7349 (tp30) REVERT: M 1424 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6796 (p90) outliers start: 74 outliers final: 62 residues processed: 667 average time/residue: 0.1924 time to fit residues: 195.2923 Evaluate side-chains 680 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 613 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 185 SER Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 446 THR Chi-restraints excluded: chain N residue 495 VAL Chi-restraints excluded: chain N residue 932 VAL Chi-restraints excluded: chain N residue 961 VAL Chi-restraints excluded: chain N residue 968 THR Chi-restraints excluded: chain N residue 969 THR Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1295 VAL Chi-restraints excluded: chain N residue 1298 ASN Chi-restraints excluded: chain N residue 1335 THR Chi-restraints excluded: chain N residue 1338 GLU Chi-restraints excluded: chain N residue 1360 GLU Chi-restraints excluded: chain N residue 1365 CYS Chi-restraints excluded: chain N residue 1404 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 303 HIS Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 445 CYS Chi-restraints excluded: chain M residue 799 ASP Chi-restraints excluded: chain M residue 807 LEU Chi-restraints excluded: chain M residue 894 LEU Chi-restraints excluded: chain M residue 961 VAL Chi-restraints excluded: chain M residue 988 ASP Chi-restraints excluded: chain M residue 1291 LEU Chi-restraints excluded: chain M residue 1307 HIS Chi-restraints excluded: chain M residue 1424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 50 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 214 optimal weight: 0.0670 chunk 255 optimal weight: 30.0000 chunk 326 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 224 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 330 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 HIS I 95 ASN ** N 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1276 ASN N1307 HIS M 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119406 restraints weight = 42023.908| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.07 r_work: 0.3179 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29304 Z= 0.173 Angle : 0.581 9.882 40014 Z= 0.304 Chirality : 0.041 0.268 4571 Planarity : 0.005 0.055 5032 Dihedral : 10.346 93.570 4624 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.67 % Allowed : 17.87 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3555 helix: 1.88 (0.12), residues: 1983 sheet: 0.29 (0.29), residues: 316 loop : -2.02 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 773 TYR 0.017 0.001 TYR N 123 PHE 0.026 0.001 PHE I 147 TRP 0.012 0.001 TRP A 134 HIS 0.006 0.001 HIS M 851 Details of bonding type rmsd covalent geometry : bond 0.00410 (29296) covalent geometry : angle 0.58078 (40008) hydrogen bonds : bond 0.04836 ( 1531) hydrogen bonds : angle 3.74911 ( 4455) metal coordination : bond 0.00819 ( 8) metal coordination : angle 1.98649 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12454.68 seconds wall clock time: 211 minutes 29.34 seconds (12689.34 seconds total)