Starting phenix.real_space_refine on Fri Aug 7 23:20:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptx_17924/08_2026/8ptx_17924.cif" } resolution = 2.87 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= 0.001 sd= 0.019 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 78 5.49 5 Mg 4 5.21 5 S 135 5.16 5 C 15197 2.51 5 N 4181 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24378 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 9667 Classifications: {'peptide': 1215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1161} Chain breaks: 3 Chain: "B" Number of atoms: 6313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6313 Classifications: {'peptide': 800} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 766} Chain breaks: 1 Chain: "C" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4296 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 29, 'TRANS': 508} Chain: "D" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2419 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 2 Chain: "X" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 59} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'5AD': 1, 'ACO': 1, 'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16664 SG CYS C 99 44.911 65.163 69.231 1.00147.46 S ATOM 16739 SG CYS C 109 43.499 61.151 74.229 1.00143.33 S ATOM 16764 SG CYS C 112 41.607 66.970 74.125 1.00140.28 S Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24378 At special positions: 0 Unit cell: (115.24, 169.42, 202.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 135 16.00 P 78 15.00 Mg 4 11.99 O 4779 8.00 N 4181 7.00 C 15197 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 112 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 109 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 99 " Number of angles added : 9 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5382 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 34 sheets defined 34.6% alpha, 23.1% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 721 through 735 removed outlier: 3.521A pdb=" N VAL A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 749 removed outlier: 3.552A pdb=" N ALA A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 759 through 766 Processing helix chain 'A' and resid 766 through 775 Processing helix chain 'A' and resid 776 through 785 Processing helix chain 'A' and resid 814 through 831 Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.545A pdb=" N LEU A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.513A pdb=" N VAL A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 863 " --> pdb=" O HIS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 Processing helix chain 'A' and resid 886 through 897 Processing helix chain 'A' and resid 899 through 909 removed outlier: 4.146A pdb=" N LYS A 909 " --> pdb=" O MET A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 926 removed outlier: 3.870A pdb=" N TYR A 917 " --> pdb=" O ASP A 913 " (cutoff:3.500A) Proline residue: A 919 - end of helix Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 969 Processing helix chain 'A' and resid 970 through 978 Processing helix chain 'A' and resid 982 through 1000 Processing helix chain 'A' and resid 1001 through 1013 Processing helix chain 'A' and resid 1014 through 1026 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1043 through 1059 Processing helix chain 'A' and resid 1061 through 1074 Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1089 through 1100 Processing helix chain 'A' and resid 1102 through 1108 removed outlier: 3.905A pdb=" N GLU A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1152 Processing helix chain 'A' and resid 1214 through 1232 Processing helix chain 'A' and resid 1232 through 1246 Processing helix chain 'A' and resid 1248 through 1274 removed outlier: 3.569A pdb=" N GLU A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Proline residue: A1271 - end of helix Processing helix chain 'B' and resid 467 through 479 removed outlier: 4.083A pdb=" N VAL B 471 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 487 Processing helix chain 'C' and resid 11 through 33 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.756A pdb=" N TYR C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.886A pdb=" N LEU C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.963A pdb=" N THR C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.026A pdb=" N SER C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 removed outlier: 3.682A pdb=" N ARG C 139 " --> pdb=" O MET C 135 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.502A pdb=" N ALA C 176 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.614A pdb=" N CYS C 227 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.541A pdb=" N GLY C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.717A pdb=" N GLU C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 382 through 395 Processing helix chain 'C' and resid 401 through 404 Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.639A pdb=" N GLY C 466 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.693A pdb=" N LEU C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 504 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'D' and resid 943 through 952 removed outlier: 3.972A pdb=" N LYS D 952 " --> pdb=" O GLY D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 956 removed outlier: 6.246A pdb=" N GLU D 956 " --> pdb=" O CYS D 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 953 through 956' Processing helix chain 'D' and resid 957 through 969 Processing helix chain 'D' and resid 970 through 978 Processing helix chain 'D' and resid 982 through 999 removed outlier: 3.519A pdb=" N GLN D 986 " --> pdb=" O SER D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1013 Processing helix chain 'D' and resid 1014 through 1025 Processing helix chain 'D' and resid 1027 through 1038 Processing helix chain 'D' and resid 1041 through 1059 removed outlier: 4.085A pdb=" N GLY D1047 " --> pdb=" O ASP D1043 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D1048 " --> pdb=" O GLN D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1072 Processing helix chain 'D' and resid 1075 through 1086 Processing helix chain 'D' and resid 1088 through 1099 Processing helix chain 'D' and resid 1102 through 1108 removed outlier: 3.826A pdb=" N GLU D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1108 through 1151 Processing helix chain 'D' and resid 1213 through 1232 removed outlier: 3.822A pdb=" N ALA D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1246 removed outlier: 3.555A pdb=" N PHE D1246 " --> pdb=" O VAL D1242 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1274 removed outlier: 3.850A pdb=" N GLY D1252 " --> pdb=" O PHE D1248 " (cutoff:3.500A) Proline residue: D1271 - end of helix Processing helix chain 'D' and resid 1311 through 1315 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 7.028A pdb=" N ASP A 372 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR A 9 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 370 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A 11 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A 368 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 3.646A pdb=" N CYS A 23 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 41 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A 43 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 50 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 76 removed outlier: 6.785A pdb=" N ALA A 86 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 74 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS A 84 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASP A 76 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER A 82 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 92 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 117 removed outlier: 4.114A pdb=" N VAL A 114 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR A 137 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 200 removed outlier: 6.054A pdb=" N ASN A 225 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 230 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'A' and resid 287 through 294 removed outlier: 7.058A pdb=" N TRP A 304 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 292 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA A 302 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 324 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 332 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 removed outlier: 4.698A pdb=" N ASP A 378 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 429 removed outlier: 3.614A pdb=" N ASP A 443 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE A 448 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG A 485 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 450 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY A 543 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 485 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 545 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 487 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 547 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLN A 489 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N SER A 549 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 545 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 534 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL A 547 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 532 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A 549 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 530 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 516 " --> pdb=" O HIS A 529 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 513 " --> pdb=" O TRP A 508 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP A 508 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 515 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 506 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 557 through 562 removed outlier: 6.699A pdb=" N GLN A 572 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 560 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 570 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 569 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 615 removed outlier: 3.643A pdb=" N ALA A 638 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 632 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 641 through 646 removed outlier: 3.841A pdb=" N SER A 643 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 696 through 701 removed outlier: 5.769A pdb=" N ILE A 697 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN A 710 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 699 " --> pdb=" O VAL A 708 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 6 through 12 removed outlier: 6.829A pdb=" N ILE B 818 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 11 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 816 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS B 810 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 784 " --> pdb=" O CYS B 810 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 24 removed outlier: 3.733A pdb=" N THR B 52 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 44 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 50 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.714A pdb=" N GLY B 81 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 64 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 79 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP B 66 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU B 77 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 78 " --> pdb=" O TRP B 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 99 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 110 through 117 removed outlier: 6.549A pdb=" N ALA B 133 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 113 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 131 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B 115 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 129 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 134 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 153 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER B 143 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS B 151 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS B 145 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 162 through 169 removed outlier: 3.609A pdb=" N ALA B 164 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 201 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA B 191 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS B 199 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLN B 193 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 210 through 218 removed outlier: 4.071A pdb=" N GLY B 212 " --> pdb=" O CYS B 227 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 224 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 233 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL B 278 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 235 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 286 through 290 removed outlier: 6.961A pdb=" N ALA B 310 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 289 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 308 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET B 316 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 333 " --> pdb=" O MET B 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 318 " --> pdb=" O GLN B 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 297 removed outlier: 3.501A pdb=" N PHE B 295 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 344 through 349 removed outlier: 6.707A pdb=" N HIS B 359 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS B 347 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 357 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE B 349 " --> pdb=" O MET B 355 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET B 355 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 396 removed outlier: 6.910A pdb=" N VAL B 406 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 394 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 404 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 432 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 416 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU B 430 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP B 418 " --> pdb=" O TRP B 428 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TRP B 428 " --> pdb=" O TRP B 418 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 441 through 448 removed outlier: 6.733A pdb=" N GLN B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 463 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 561 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER B 465 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU B 559 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AC9, first strand: chain 'B' and resid 570 through 572 removed outlier: 6.629A pdb=" N ALA B 585 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 595 through 598 removed outlier: 4.032A pdb=" N GLN B 608 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 617 through 622 removed outlier: 7.065A pdb=" N VAL B 632 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 620 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 630 " --> pdb=" O MET B 620 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE B 622 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 628 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP B 638 " --> pdb=" O PHE B 660 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE B 660 " --> pdb=" O TRP B 638 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 640 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 672 through 677 removed outlier: 3.518A pdb=" N GLY B 697 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 711 " --> pdb=" O GLY B 697 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 723 through 728 removed outlier: 3.956A pdb=" N ALA B 725 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR B 753 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B 768 " --> pdb=" O THR B 753 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 88 through 93 removed outlier: 7.882A pdb=" N VAL C 165 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 218 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE C 167 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE C 220 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 169 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 241 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 218 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU C 243 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 220 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE C 245 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 282 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY C 246 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS C 284 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEU C 315 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 322 through 323 removed outlier: 7.178A pdb=" N VAL C 322 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 421 through 429 removed outlier: 7.180A pdb=" N TRP C 433 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG C 454 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 435 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG C 452 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 437 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 450 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR C 439 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 474 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG C 454 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 472 " --> pdb=" O ARG C 454 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 10400 1.41 - 1.63: 14485 1.63 - 1.85: 185 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 25082 Sorted by residual: bond pdb=" C ACO C 603 " pdb=" CH3 ACO C 603 " ideal model delta sigma weight residual 1.500 1.462 0.038 1.00e-02 1.00e+04 1.41e+01 bond pdb=" C2P ACO C 603 " pdb=" S1P ACO C 603 " ideal model delta sigma weight residual 1.818 1.782 0.036 1.00e-02 1.00e+04 1.29e+01 bond pdb=" N GLN C 248 " pdb=" CA GLN C 248 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" P U X 72 " pdb=" O5' U X 72 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 7.64e+00 bond pdb=" C3B ACO C 603 " pdb=" O3B ACO C 603 " ideal model delta sigma weight residual 1.444 1.412 0.032 1.20e-02 6.94e+03 7.20e+00 ... (remaining 25077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 34352 5.21 - 10.43: 45 10.43 - 15.64: 1 15.64 - 20.86: 0 20.86 - 26.07: 1 Bond angle restraints: 34399 Sorted by residual: angle pdb=" C ACO C 603 " pdb=" S1P ACO C 603 " pdb=" C2P ACO C 603 " ideal model delta sigma weight residual 101.25 127.32 -26.07 1.00e+00 1.00e+00 6.80e+02 angle pdb=" P1A ACO C 603 " pdb=" O3A ACO C 603 " pdb=" P2A ACO C 603 " ideal model delta sigma weight residual 136.83 128.63 8.20 1.00e+00 1.00e+00 6.72e+01 angle pdb=" C3B ACO C 603 " pdb=" O3B ACO C 603 " pdb=" P3B ACO C 603 " ideal model delta sigma weight residual 121.12 115.28 5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" C SER A 808 " pdb=" CA SER A 808 " pdb=" CB SER A 808 " ideal model delta sigma weight residual 116.54 110.13 6.41 1.15e+00 7.56e-01 3.11e+01 angle pdb=" N GLU A 916 " pdb=" CA GLU A 916 " pdb=" C GLU A 916 " ideal model delta sigma weight residual 114.62 108.40 6.22 1.14e+00 7.69e-01 2.98e+01 ... (remaining 34394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 14719 35.57 - 71.14: 412 71.14 - 106.70: 40 106.70 - 142.27: 1 142.27 - 177.84: 2 Dihedral angle restraints: 15174 sinusoidal: 6867 harmonic: 8307 Sorted by residual: dihedral pdb=" O4' G X 18 " pdb=" C2' G X 18 " pdb=" C1' G X 18 " pdb=" C3' G X 18 " ideal model delta sinusoidal sigma weight residual -35.00 22.98 -57.98 1 8.00e+00 1.56e-02 7.05e+01 dihedral pdb=" C4' G X 18 " pdb=" O4' G X 18 " pdb=" C1' G X 18 " pdb=" C2' G X 18 " ideal model delta sinusoidal sigma weight residual -21.00 33.70 -54.70 1 8.00e+00 1.56e-02 6.33e+01 dihedral pdb=" O4' U X 19 " pdb=" C1' U X 19 " pdb=" N1 U X 19 " pdb=" C2 U X 19 " ideal model delta sinusoidal sigma weight residual -160.00 -60.56 -99.44 1 1.50e+01 4.44e-03 4.97e+01 ... (remaining 15171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3682 0.103 - 0.206: 213 0.206 - 0.309: 3 0.309 - 0.412: 2 0.412 - 0.515: 7 Chirality restraints: 3907 Sorted by residual: chirality pdb=" P U X 19 " pdb=" OP1 U X 19 " pdb=" OP2 U X 19 " pdb=" O5' U X 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P C X 71 " pdb=" OP1 C X 71 " pdb=" OP2 C X 71 " pdb=" O5' C X 71 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" P A X 14 " pdb=" OP1 A X 14 " pdb=" OP2 A X 14 " pdb=" O5' A X 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 3904 not shown) Planarity restraints: 4126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO C 603 " 0.337 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C5P ACO C 603 " -0.090 2.00e-02 2.50e+03 pdb=" C6P ACO C 603 " 0.049 2.00e-02 2.50e+03 pdb=" N4P ACO C 603 " -0.506 2.00e-02 2.50e+03 pdb=" O5P ACO C 603 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C 603 " 0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C9P ACO C 603 " -0.060 2.00e-02 2.50e+03 pdb=" CAP ACO C 603 " 0.128 2.00e-02 2.50e+03 pdb=" N8P ACO C 603 " -0.219 2.00e-02 2.50e+03 pdb=" O9P ACO C 603 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 247 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C VAL C 247 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL C 247 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 248 " -0.013 2.00e-02 2.50e+03 ... (remaining 4123 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4097 2.77 - 3.30: 22258 3.30 - 3.83: 38930 3.83 - 4.37: 45847 4.37 - 4.90: 79511 Nonbonded interactions: 190643 Sorted by model distance: nonbonded pdb=" NH2 ARG A1011 " pdb=" O PHE D1244 " model vdw 2.233 3.120 nonbonded pdb=" O ILE B 671 " pdb=" OG SER B 688 " model vdw 2.243 3.040 nonbonded pdb=" O ALA C 509 " pdb=" OG SER C 515 " model vdw 2.247 3.040 nonbonded pdb=" O2' A X 57 " pdb=" OP2 U X 59 " model vdw 2.271 3.040 nonbonded pdb=" NE2 GLN A 309 " pdb=" O GLU A 311 " model vdw 2.271 3.120 ... (remaining 190638 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 11.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.004 0.051 25085 Z= 0.195 Angle : 0.688 26.071 34408 Z= 0.434 Chirality : 0.052 0.515 3907 Planarity : 0.007 0.291 4126 Dihedral : 15.844 177.841 9792 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 2831 helix: 1.35 (0.17), residues: 910 sheet: 0.08 (0.20), residues: 631 loop : -1.89 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1011 TYR 0.027 0.001 TYR C 122 PHE 0.018 0.002 PHE A1022 TRP 0.020 0.001 TRP A 224 HIS 0.008 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (25082) covalent geometry : angle 0.68225 / 0.43 (34399) hydrogen bonds : bond 0.14526 / 9.77 ( 1022) hydrogen bonds : angle 5.79774 / 4.09 ( 2869) metal coordination : bond 0.00535 / 0.27 ( 3) metal coordination : angle 5.41947 / 2.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 451 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.6028 (pp20) cc_final: 0.5277 (pp20) REVERT: A 141 GLU cc_start: 0.7732 (tp30) cc_final: 0.7407 (tp30) REVERT: A 156 SER cc_start: 0.7271 (t) cc_final: 0.7028 (t) REVERT: A 227 GLU cc_start: 0.7663 (mp0) cc_final: 0.7401 (mp0) REVERT: A 291 ASP cc_start: 0.7909 (t0) cc_final: 0.7658 (t0) REVERT: A 476 CYS cc_start: 0.8075 (m) cc_final: 0.7753 (t) REVERT: A 487 LYS cc_start: 0.7619 (tppt) cc_final: 0.7224 (ttpp) REVERT: A 511 GLU cc_start: 0.7910 (tt0) cc_final: 0.7702 (tt0) REVERT: A 521 GLU cc_start: 0.7524 (pm20) cc_final: 0.7217 (pm20) REVERT: A 525 ARG cc_start: 0.6989 (ttp-170) cc_final: 0.6783 (ttm-80) REVERT: A 544 GLN cc_start: 0.7826 (tt0) cc_final: 0.7425 (tt0) REVERT: A 567 LYS cc_start: 0.7941 (mttm) cc_final: 0.7581 (mtpm) REVERT: A 617 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 666 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6489 (mtm-85) REVERT: A 690 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7645 (mttp) REVERT: A 696 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7684 (mtm-85) REVERT: A 743 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7039 (mp0) REVERT: A 789 GLU cc_start: 0.6661 (tp30) cc_final: 0.5834 (tp30) REVERT: A 795 THR cc_start: 0.7354 (p) cc_final: 0.7137 (p) REVERT: A 976 LYS cc_start: 0.8633 (tptp) cc_final: 0.8264 (ttmm) REVERT: A 1266 MET cc_start: 0.8754 (mtt) cc_final: 0.8430 (mtt) REVERT: B 29 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7195 (mtm110) REVERT: B 39 SER cc_start: 0.7991 (m) cc_final: 0.7666 (t) REVERT: B 71 ASP cc_start: 0.7681 (m-30) cc_final: 0.6894 (p0) REVERT: B 73 SER cc_start: 0.8197 (m) cc_final: 0.7285 (p) REVERT: B 193 GLN cc_start: 0.6275 (pp30) cc_final: 0.5751 (pp30) REVERT: B 198 GLN cc_start: 0.7569 (mt0) cc_final: 0.7344 (mt0) REVERT: B 254 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7296 (mtm110) REVERT: B 300 VAL cc_start: 0.6459 (m) cc_final: 0.6244 (p) REVERT: B 303 GLN cc_start: 0.7282 (tt0) cc_final: 0.6936 (tt0) REVERT: B 314 LYS cc_start: 0.7131 (mmtt) cc_final: 0.6578 (mttp) REVERT: B 356 ILE cc_start: 0.7529 (mt) cc_final: 0.7193 (mm) REVERT: B 423 GLN cc_start: 0.4705 (tm-30) cc_final: 0.4337 (tm-30) REVERT: B 425 GLN cc_start: 0.6894 (tt0) cc_final: 0.6651 (pt0) REVERT: B 443 CYS cc_start: 0.7716 (m) cc_final: 0.7156 (p) REVERT: B 457 ASP cc_start: 0.7346 (t0) cc_final: 0.6828 (t0) REVERT: B 587 LYS cc_start: 0.8169 (mttm) cc_final: 0.7931 (mttm) REVERT: B 591 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7417 (ttmm) REVERT: B 642 LYS cc_start: 0.6531 (tttm) cc_final: 0.6230 (ttpt) REVERT: B 677 TRP cc_start: 0.7674 (m100) cc_final: 0.7188 (m100) REVERT: C 24 LYS cc_start: 0.8098 (tptp) cc_final: 0.7772 (tptp) REVERT: C 36 ILE cc_start: 0.6843 (tt) cc_final: 0.6580 (tt) REVERT: C 73 MET cc_start: 0.6884 (mmp) cc_final: 0.6660 (mpp) REVERT: C 98 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7365 (mtt-85) REVERT: C 130 TYR cc_start: 0.7884 (m-80) cc_final: 0.7114 (m-80) REVERT: C 259 ASN cc_start: 0.8500 (t0) cc_final: 0.8022 (t0) REVERT: C 313 ASP cc_start: 0.7918 (m-30) cc_final: 0.7703 (m-30) REVERT: C 368 ASP cc_start: 0.8210 (t0) cc_final: 0.7394 (t0) REVERT: D 1044 GLN cc_start: 0.5539 (tt0) cc_final: 0.5077 (mt0) REVERT: D 1121 MET cc_start: 0.7846 (mmp) cc_final: 0.7448 (mmt) outliers start: 1 outliers final: 2 residues processed: 452 average time/residue: 0.6279 time to fit residues: 326.1351 Evaluate side-chains 403 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 92 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 271 ASN A 489 GLN A 544 GLN A 572 GLN A 751 ASN A 888 ASN A 972 ASN B 182 ASN B 188 HIS B 292 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 662 ASN B 776 GLN D1108 ASN D1238 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111285 restraints weight = 37240.569| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.35 r_work: 0.3307 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25085 Z= 0.162 Angle : 0.633 9.928 34408 Z= 0.332 Chirality : 0.045 0.320 3907 Planarity : 0.005 0.049 4126 Dihedral : 15.240 163.526 4311 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.75 % Allowed : 9.13 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 2831 helix: 1.29 (0.17), residues: 923 sheet: 0.19 (0.20), residues: 637 loop : -1.84 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1011 TYR 0.015 0.001 TYR B 564 PHE 0.026 0.002 PHE D1131 TRP 0.014 0.002 TRP B 215 HIS 0.008 0.001 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25082) covalent geometry : angle 0.62697 / 0.33 (34399) hydrogen bonds : bond 0.05331 / 3.58 ( 1022) hydrogen bonds : angle 4.80281 / 3.35 ( 2869) metal coordination : bond 0.00605 / 0.30 ( 3) metal coordination : angle 5.27444 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 408 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7115 (pp20) cc_final: 0.6622 (pp20) REVERT: A 187 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 521 GLU cc_start: 0.8087 (pm20) cc_final: 0.7817 (pm20) REVERT: A 567 LYS cc_start: 0.8432 (mttm) cc_final: 0.8207 (mtpm) REVERT: A 582 LEU cc_start: 0.9037 (mp) cc_final: 0.8833 (mt) REVERT: A 602 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8439 (ttt180) REVERT: A 666 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: A 690 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8208 (mttp) REVERT: A 743 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8072 (mp0) REVERT: A 789 GLU cc_start: 0.7310 (tp30) cc_final: 0.6881 (tp30) REVERT: A 916 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 976 LYS cc_start: 0.8767 (tptp) cc_final: 0.8482 (tppp) REVERT: A 1001 MET cc_start: 0.5540 (mmm) cc_final: 0.5015 (mpm) REVERT: B 29 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7638 (mtm110) REVERT: B 71 ASP cc_start: 0.7992 (m-30) cc_final: 0.7663 (p0) REVERT: B 73 SER cc_start: 0.8816 (m) cc_final: 0.8122 (p) REVERT: B 193 GLN cc_start: 0.7278 (pp30) cc_final: 0.6946 (pp30) REVERT: B 195 ASP cc_start: 0.8188 (m-30) cc_final: 0.7525 (t0) REVERT: B 269 ILE cc_start: 0.8104 (mm) cc_final: 0.7849 (mm) REVERT: B 395 VAL cc_start: 0.8938 (t) cc_final: 0.8724 (m) REVERT: B 399 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6563 (mt-10) REVERT: B 401 GLU cc_start: 0.7737 (mp0) cc_final: 0.6750 (mp0) REVERT: B 423 GLN cc_start: 0.5839 (tm-30) cc_final: 0.5583 (tm-30) REVERT: B 457 ASP cc_start: 0.8092 (t0) cc_final: 0.7724 (t0) REVERT: B 591 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8289 (ttmm) REVERT: B 615 LEU cc_start: 0.7940 (mm) cc_final: 0.7700 (mm) REVERT: B 642 LYS cc_start: 0.8237 (tttm) cc_final: 0.8027 (ttpt) REVERT: C 24 LYS cc_start: 0.8905 (tptp) cc_final: 0.8527 (tptp) REVERT: C 98 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8264 (mtt-85) REVERT: C 130 TYR cc_start: 0.8804 (m-80) cc_final: 0.8198 (m-80) REVERT: C 228 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7561 (mmm) REVERT: C 259 ASN cc_start: 0.8742 (t0) cc_final: 0.8495 (t0) REVERT: C 347 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: C 368 ASP cc_start: 0.8213 (t0) cc_final: 0.7677 (t0) REVERT: C 380 HIS cc_start: 0.7746 (m-70) cc_final: 0.7489 (m-70) REVERT: C 458 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: D 1044 GLN cc_start: 0.6915 (tt0) cc_final: 0.6035 (mt0) REVERT: D 1061 LYS cc_start: 0.7211 (mmmt) cc_final: 0.6896 (mmmt) REVERT: D 1121 MET cc_start: 0.7274 (mmp) cc_final: 0.6958 (mmt) REVERT: D 1263 LEU cc_start: 0.7935 (pp) cc_final: 0.7500 (mp) outliers start: 44 outliers final: 17 residues processed: 425 average time/residue: 0.5806 time to fit residues: 283.4057 Evaluate side-chains 414 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 392 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 458 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 194 optimal weight: 0.0870 chunk 255 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 329 HIS ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN A1044 GLN B 53 ASN B 194 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 814 HIS C 199 ASN D 963 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110274 restraints weight = 37113.393| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.35 r_work: 0.3290 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25085 Z= 0.191 Angle : 0.636 11.349 34408 Z= 0.335 Chirality : 0.046 0.231 3907 Planarity : 0.005 0.070 4126 Dihedral : 14.954 162.692 4308 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.59 % Allowed : 11.72 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2831 helix: 1.26 (0.17), residues: 923 sheet: 0.19 (0.20), residues: 643 loop : -1.90 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 69 TYR 0.015 0.002 TYR A 416 PHE 0.021 0.002 PHE A 278 TRP 0.017 0.002 TRP B 215 HIS 0.009 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (25082) covalent geometry : angle 0.63039 / 0.33 (34399) hydrogen bonds : bond 0.05481 / 3.65 ( 1022) hydrogen bonds : angle 4.67205 / 3.26 ( 2869) metal coordination : bond 0.00716 / 0.36 ( 3) metal coordination : angle 5.43339 / 2.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7428 (pp20) cc_final: 0.6962 (tm-30) REVERT: A 187 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 227 GLU cc_start: 0.8488 (mp0) cc_final: 0.8111 (mp0) REVERT: A 521 GLU cc_start: 0.8099 (pm20) cc_final: 0.7816 (pm20) REVERT: A 567 LYS cc_start: 0.8466 (mttm) cc_final: 0.8241 (mtpm) REVERT: A 602 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (ttt180) REVERT: A 743 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8064 (mp0) REVERT: A 789 GLU cc_start: 0.7404 (tp30) cc_final: 0.6967 (tp30) REVERT: A 916 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7186 (tm-30) REVERT: A 976 LYS cc_start: 0.8788 (tptp) cc_final: 0.8470 (tppp) REVERT: A 1001 MET cc_start: 0.5579 (mmm) cc_final: 0.5120 (mpm) REVERT: B 29 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7601 (mtm110) REVERT: B 71 ASP cc_start: 0.8010 (m-30) cc_final: 0.7666 (p0) REVERT: B 73 SER cc_start: 0.8824 (m) cc_final: 0.8155 (p) REVERT: B 193 GLN cc_start: 0.7243 (pp30) cc_final: 0.7012 (pp30) REVERT: B 195 ASP cc_start: 0.8258 (m-30) cc_final: 0.7606 (t0) REVERT: B 261 THR cc_start: 0.8604 (p) cc_final: 0.8369 (t) REVERT: B 302 GLN cc_start: 0.7891 (mp10) cc_final: 0.7484 (mp10) REVERT: B 334 VAL cc_start: 0.8871 (t) cc_final: 0.8563 (p) REVERT: B 356 ILE cc_start: 0.8391 (mm) cc_final: 0.8135 (mt) REVERT: B 399 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6546 (mt-10) REVERT: B 401 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: B 457 ASP cc_start: 0.8119 (t0) cc_final: 0.7775 (t0) REVERT: B 552 LEU cc_start: 0.8473 (tp) cc_final: 0.8213 (tp) REVERT: B 591 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8331 (ttmm) REVERT: B 642 LYS cc_start: 0.8292 (tttm) cc_final: 0.8040 (ttpt) REVERT: C 24 LYS cc_start: 0.8892 (tptp) cc_final: 0.8523 (tptp) REVERT: C 73 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: C 98 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8302 (mtt-85) REVERT: C 130 TYR cc_start: 0.8804 (m-80) cc_final: 0.8227 (m-80) REVERT: C 163 ASP cc_start: 0.7785 (t0) cc_final: 0.7550 (t0) REVERT: C 228 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7562 (mmm) REVERT: C 248 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7011 (mt0) REVERT: C 259 ASN cc_start: 0.8775 (t0) cc_final: 0.8553 (t0) REVERT: C 347 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: C 368 ASP cc_start: 0.8098 (t0) cc_final: 0.7585 (t0) REVERT: C 380 HIS cc_start: 0.7812 (m-70) cc_final: 0.7546 (m-70) REVERT: C 385 GLU cc_start: 0.7968 (pt0) cc_final: 0.7755 (mt-10) REVERT: C 458 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 999 GLU cc_start: 0.5001 (mm-30) cc_final: 0.4355 (tm-30) REVERT: D 1044 GLN cc_start: 0.6940 (tt0) cc_final: 0.5747 (pt0) REVERT: D 1121 MET cc_start: 0.7652 (mmp) cc_final: 0.7423 (mmt) REVERT: D 1124 LEU cc_start: 0.8750 (tm) cc_final: 0.8499 (pp) REVERT: D 1263 LEU cc_start: 0.7951 (pp) cc_final: 0.7579 (mp) outliers start: 65 outliers final: 26 residues processed: 431 average time/residue: 0.5901 time to fit residues: 294.4729 Evaluate side-chains 426 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 392 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1042 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 814 HIS ** D1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110111 restraints weight = 36735.704| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.39 r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25085 Z= 0.187 Angle : 0.621 12.140 34408 Z= 0.327 Chirality : 0.045 0.189 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.836 165.825 4306 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.79 % Allowed : 13.43 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2831 helix: 1.28 (0.17), residues: 929 sheet: 0.17 (0.20), residues: 643 loop : -1.94 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 525 TYR 0.017 0.002 TYR B 752 PHE 0.021 0.002 PHE A 207 TRP 0.018 0.002 TRP B 215 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (25082) covalent geometry : angle 0.61471 / 0.33 (34399) hydrogen bonds : bond 0.05309 / 3.53 ( 1022) hydrogen bonds : angle 4.59311 / 3.21 ( 2869) metal coordination : bond 0.00745 / 0.38 ( 3) metal coordination : angle 5.63160 / 2.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 397 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8737 (t80) cc_final: 0.8478 (t80) REVERT: A 65 GLU cc_start: 0.8366 (pm20) cc_final: 0.7821 (pp20) REVERT: A 81 GLU cc_start: 0.7218 (pp20) cc_final: 0.6739 (pp20) REVERT: A 187 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 227 GLU cc_start: 0.8500 (mp0) cc_final: 0.8129 (mp0) REVERT: A 471 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 567 LYS cc_start: 0.8461 (mttm) cc_final: 0.8252 (mtpm) REVERT: A 602 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8476 (ttt180) REVERT: A 666 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7557 (mtm-85) REVERT: A 743 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8051 (mp0) REVERT: A 789 GLU cc_start: 0.7449 (tp30) cc_final: 0.7003 (tp30) REVERT: A 916 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 976 LYS cc_start: 0.8779 (tptp) cc_final: 0.8442 (tppp) REVERT: A 1001 MET cc_start: 0.5642 (mmm) cc_final: 0.5202 (mpm) REVERT: A 1019 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7281 (mm) REVERT: B 18 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8365 (t) REVERT: B 29 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7629 (mtm110) REVERT: B 71 ASP cc_start: 0.8030 (m-30) cc_final: 0.7643 (p0) REVERT: B 73 SER cc_start: 0.8822 (m) cc_final: 0.8052 (p) REVERT: B 193 GLN cc_start: 0.7272 (pp30) cc_final: 0.6992 (pp30) REVERT: B 195 ASP cc_start: 0.8277 (m-30) cc_final: 0.7607 (t0) REVERT: B 261 THR cc_start: 0.8636 (p) cc_final: 0.8378 (t) REVERT: B 269 ILE cc_start: 0.8116 (mm) cc_final: 0.7852 (mm) REVERT: B 302 GLN cc_start: 0.7812 (mp10) cc_final: 0.7429 (mp10) REVERT: B 334 VAL cc_start: 0.8892 (t) cc_final: 0.8610 (p) REVERT: B 356 ILE cc_start: 0.8428 (mm) cc_final: 0.8168 (mt) REVERT: B 399 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6504 (mt-10) REVERT: B 401 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: B 457 ASP cc_start: 0.8130 (t0) cc_final: 0.7818 (t0) REVERT: B 555 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 642 LYS cc_start: 0.8292 (tttm) cc_final: 0.8050 (ttpt) REVERT: C 24 LYS cc_start: 0.8888 (tptp) cc_final: 0.8530 (tptp) REVERT: C 98 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8306 (mtt-85) REVERT: C 130 TYR cc_start: 0.8802 (m-80) cc_final: 0.8190 (m-80) REVERT: C 163 ASP cc_start: 0.7796 (t0) cc_final: 0.7573 (t0) REVERT: C 184 TYR cc_start: 0.8276 (t80) cc_final: 0.7938 (t80) REVERT: C 248 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: C 259 ASN cc_start: 0.8781 (t0) cc_final: 0.8566 (t0) REVERT: C 347 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 368 ASP cc_start: 0.8085 (t0) cc_final: 0.7571 (t0) REVERT: C 380 HIS cc_start: 0.7818 (m-70) cc_final: 0.7560 (m-70) REVERT: C 385 GLU cc_start: 0.7937 (pt0) cc_final: 0.7713 (mt-10) REVERT: C 458 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: D 999 GLU cc_start: 0.5086 (mm-30) cc_final: 0.4459 (tm-30) REVERT: D 1044 GLN cc_start: 0.6957 (tt0) cc_final: 0.5863 (pt0) REVERT: D 1061 LYS cc_start: 0.7470 (tptt) cc_final: 0.7199 (pttt) REVERT: D 1121 MET cc_start: 0.7787 (mmp) cc_final: 0.7401 (mmt) REVERT: D 1263 LEU cc_start: 0.7951 (pp) cc_final: 0.7593 (mp) outliers start: 70 outliers final: 37 residues processed: 429 average time/residue: 0.6178 time to fit residues: 306.2998 Evaluate side-chains 431 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 384 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1042 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 57 optimal weight: 0.0040 chunk 109 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 198 GLN B 366 HIS ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 HIS C 307 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109816 restraints weight = 36636.849| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.44 r_work: 0.3276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25085 Z= 0.213 Angle : 0.647 13.530 34408 Z= 0.338 Chirality : 0.046 0.197 3907 Planarity : 0.005 0.062 4126 Dihedral : 14.752 171.244 4306 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.15 % Allowed : 14.03 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 2831 helix: 1.28 (0.17), residues: 933 sheet: 0.06 (0.20), residues: 655 loop : -1.98 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.017 0.002 TYR B 752 PHE 0.023 0.002 PHE A 207 TRP 0.019 0.002 TRP B 215 HIS 0.009 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (25082) covalent geometry : angle 0.63879 / 0.34 (34399) hydrogen bonds : bond 0.05558 / 3.67 ( 1022) hydrogen bonds : angle 4.57861 / 3.19 ( 2869) metal coordination : bond 0.00846 / 0.43 ( 3) metal coordination : angle 6.39460 / 2.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 403 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8747 (t80) cc_final: 0.8485 (t80) REVERT: A 65 GLU cc_start: 0.8374 (pm20) cc_final: 0.7809 (pp20) REVERT: A 81 GLU cc_start: 0.7343 (pp20) cc_final: 0.6854 (pp20) REVERT: A 227 GLU cc_start: 0.8533 (mp0) cc_final: 0.8044 (mp0) REVERT: A 471 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 475 VAL cc_start: 0.8721 (p) cc_final: 0.8401 (t) REVERT: A 521 GLU cc_start: 0.8018 (pm20) cc_final: 0.7748 (pm20) REVERT: A 567 LYS cc_start: 0.8446 (mttm) cc_final: 0.8232 (mtpm) REVERT: A 602 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (ttt180) REVERT: A 666 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7538 (mtm-85) REVERT: A 743 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8092 (mp0) REVERT: A 789 GLU cc_start: 0.7540 (tp30) cc_final: 0.7109 (tp30) REVERT: A 916 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 976 LYS cc_start: 0.8810 (tptp) cc_final: 0.8442 (tppp) REVERT: A 1001 MET cc_start: 0.5749 (mmm) cc_final: 0.5310 (mpm) REVERT: A 1019 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7244 (mm) REVERT: B 18 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8295 (m) REVERT: B 29 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7647 (mtm110) REVERT: B 71 ASP cc_start: 0.8055 (m-30) cc_final: 0.7564 (p0) REVERT: B 73 SER cc_start: 0.8806 (m) cc_final: 0.8023 (m) REVERT: B 193 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7027 (pp30) REVERT: B 195 ASP cc_start: 0.8269 (m-30) cc_final: 0.7601 (t0) REVERT: B 261 THR cc_start: 0.8679 (p) cc_final: 0.8411 (t) REVERT: B 269 ILE cc_start: 0.8202 (mm) cc_final: 0.7928 (mm) REVERT: B 334 VAL cc_start: 0.8918 (t) cc_final: 0.8660 (p) REVERT: B 356 ILE cc_start: 0.8472 (mm) cc_final: 0.8209 (mt) REVERT: B 399 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6635 (mt-10) REVERT: B 401 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 420 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8234 (mtm-85) REVERT: B 457 ASP cc_start: 0.8153 (t0) cc_final: 0.7829 (t0) REVERT: B 555 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 591 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8500 (ttmm) REVERT: B 764 ASN cc_start: 0.6316 (t0) cc_final: 0.6001 (t0) REVERT: C 24 LYS cc_start: 0.8895 (tptp) cc_final: 0.8530 (tptp) REVERT: C 73 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7601 (mpp) REVERT: C 98 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8282 (mtt-85) REVERT: C 130 TYR cc_start: 0.8800 (m-80) cc_final: 0.8218 (m-80) REVERT: C 175 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: C 184 TYR cc_start: 0.8288 (t80) cc_final: 0.7992 (t80) REVERT: C 228 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7506 (mmm) REVERT: C 259 ASN cc_start: 0.8787 (t0) cc_final: 0.8526 (t0) REVERT: C 347 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: C 368 ASP cc_start: 0.8100 (t0) cc_final: 0.7570 (t0) REVERT: C 380 HIS cc_start: 0.7835 (m-70) cc_final: 0.7562 (m-70) REVERT: C 385 GLU cc_start: 0.7920 (pt0) cc_final: 0.7714 (mt-10) REVERT: C 447 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7850 (tt) REVERT: C 458 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: D 999 GLU cc_start: 0.5056 (mm-30) cc_final: 0.4478 (tm-30) REVERT: D 1044 GLN cc_start: 0.7053 (tt0) cc_final: 0.5962 (pt0) REVERT: D 1082 LEU cc_start: 0.6019 (mt) cc_final: 0.5601 (mp) REVERT: D 1121 MET cc_start: 0.7966 (mmp) cc_final: 0.7463 (mmt) REVERT: D 1263 LEU cc_start: 0.7932 (pp) cc_final: 0.7598 (mp) outliers start: 79 outliers final: 44 residues processed: 437 average time/residue: 0.6220 time to fit residues: 313.4212 Evaluate side-chains 444 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 387 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1042 LYS Chi-restraints excluded: chain D residue 1108 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 216 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 193 GLN B 593 HIS B 814 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110360 restraints weight = 36579.786| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.39 r_work: 0.3290 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25085 Z= 0.167 Angle : 0.617 13.403 34408 Z= 0.322 Chirality : 0.045 0.179 3907 Planarity : 0.005 0.062 4126 Dihedral : 14.679 168.892 4306 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.99 % Allowed : 15.07 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2831 helix: 1.34 (0.17), residues: 933 sheet: -0.00 (0.20), residues: 666 loop : -1.96 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 525 TYR 0.016 0.001 TYR B 752 PHE 0.020 0.002 PHE A 207 TRP 0.048 0.002 TRP B 677 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (25082) covalent geometry : angle 0.60851 / 0.32 (34399) hydrogen bonds : bond 0.05110 / 3.38 ( 1022) hydrogen bonds : angle 4.53880 / 3.16 ( 2869) metal coordination : bond 0.00649 / 0.33 ( 3) metal coordination : angle 6.21974 / 2.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 390 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8749 (t80) cc_final: 0.8475 (t80) REVERT: A 65 GLU cc_start: 0.8365 (pm20) cc_final: 0.7792 (pp20) REVERT: A 81 GLU cc_start: 0.7284 (pp20) cc_final: 0.6796 (pp20) REVERT: A 227 GLU cc_start: 0.8523 (mp0) cc_final: 0.8152 (mp0) REVERT: A 471 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 521 GLU cc_start: 0.7987 (pm20) cc_final: 0.7728 (pm20) REVERT: A 567 LYS cc_start: 0.8427 (mttm) cc_final: 0.8212 (mtpm) REVERT: A 602 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8506 (ttt180) REVERT: A 666 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: A 743 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8075 (mp0) REVERT: A 789 GLU cc_start: 0.7553 (tp30) cc_final: 0.7124 (tp30) REVERT: A 916 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 976 LYS cc_start: 0.8805 (tptp) cc_final: 0.8430 (tppp) REVERT: A 1001 MET cc_start: 0.5728 (mmm) cc_final: 0.5311 (mpm) REVERT: A 1019 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7241 (mm) REVERT: B 29 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7647 (mtm110) REVERT: B 71 ASP cc_start: 0.8044 (m-30) cc_final: 0.7561 (p0) REVERT: B 73 SER cc_start: 0.8794 (m) cc_final: 0.8099 (m) REVERT: B 193 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: B 195 ASP cc_start: 0.8241 (m-30) cc_final: 0.7665 (t0) REVERT: B 198 GLN cc_start: 0.8713 (mt0) cc_final: 0.8449 (mt0) REVERT: B 334 VAL cc_start: 0.8917 (t) cc_final: 0.8673 (p) REVERT: B 356 ILE cc_start: 0.8459 (mm) cc_final: 0.8185 (mt) REVERT: B 399 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 401 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: B 457 ASP cc_start: 0.8110 (t0) cc_final: 0.7797 (t0) REVERT: B 555 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8047 (p) REVERT: B 591 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8492 (ttmm) REVERT: B 642 LYS cc_start: 0.8253 (tttp) cc_final: 0.8047 (ttpt) REVERT: B 813 ASP cc_start: 0.7879 (p0) cc_final: 0.7604 (p0) REVERT: C 24 LYS cc_start: 0.8895 (tptp) cc_final: 0.8535 (tptp) REVERT: C 98 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8277 (mtt-85) REVERT: C 130 TYR cc_start: 0.8783 (m-80) cc_final: 0.8197 (m-80) REVERT: C 184 TYR cc_start: 0.8237 (t80) cc_final: 0.7931 (t80) REVERT: C 259 ASN cc_start: 0.8773 (t0) cc_final: 0.8536 (t0) REVERT: C 347 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: C 368 ASP cc_start: 0.8038 (t0) cc_final: 0.7534 (t0) REVERT: C 458 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: D 1044 GLN cc_start: 0.7051 (tt0) cc_final: 0.5933 (pt0) REVERT: D 1061 LYS cc_start: 0.7374 (tptt) cc_final: 0.7151 (tptt) REVERT: D 1121 MET cc_start: 0.7974 (mmp) cc_final: 0.7639 (mmt) REVERT: D 1245 LEU cc_start: 0.7736 (tp) cc_final: 0.7454 (tm) REVERT: D 1263 LEU cc_start: 0.7937 (pp) cc_final: 0.7598 (mp) outliers start: 75 outliers final: 47 residues processed: 422 average time/residue: 0.5826 time to fit residues: 283.2776 Evaluate side-chains 441 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 386 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1042 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 214 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 HIS A 446 ASN A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 814 HIS D1127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109296 restraints weight = 36675.522| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.30 r_work: 0.3274 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25085 Z= 0.254 Angle : 0.681 14.560 34408 Z= 0.354 Chirality : 0.048 0.314 3907 Planarity : 0.005 0.065 4126 Dihedral : 14.663 169.597 4306 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.35 % Allowed : 15.58 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2831 helix: 1.20 (0.17), residues: 935 sheet: -0.11 (0.19), residues: 693 loop : -2.03 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 306 TYR 0.020 0.002 TYR B 752 PHE 0.025 0.002 PHE A 207 TRP 0.037 0.002 TRP B 677 HIS 0.009 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.25 (25082) covalent geometry : angle 0.67098 / 0.35 (34399) hydrogen bonds : bond 0.05859 / 3.86 ( 1022) hydrogen bonds : angle 4.63733 / 3.23 ( 2869) metal coordination : bond 0.00983 / 0.50 ( 3) metal coordination : angle 7.06784 / 3.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 399 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8750 (t80) cc_final: 0.8497 (t80) REVERT: A 65 GLU cc_start: 0.8378 (pm20) cc_final: 0.7853 (pp20) REVERT: A 81 GLU cc_start: 0.7331 (pp20) cc_final: 0.6881 (pp20) REVERT: A 227 GLU cc_start: 0.8538 (mp0) cc_final: 0.8139 (mp0) REVERT: A 471 SER cc_start: 0.8483 (p) cc_final: 0.8259 (t) REVERT: A 475 VAL cc_start: 0.8733 (p) cc_final: 0.8421 (t) REVERT: A 521 GLU cc_start: 0.7968 (pm20) cc_final: 0.7706 (pm20) REVERT: A 567 LYS cc_start: 0.8430 (mttm) cc_final: 0.8221 (mtpm) REVERT: A 602 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8449 (ttt180) REVERT: A 666 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: A 743 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8081 (mp0) REVERT: A 789 GLU cc_start: 0.7582 (tp30) cc_final: 0.7154 (tp30) REVERT: A 842 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7830 (t) REVERT: A 916 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 976 LYS cc_start: 0.8822 (tptp) cc_final: 0.8443 (tppp) REVERT: A 1001 MET cc_start: 0.5814 (mmm) cc_final: 0.5395 (mpm) REVERT: A 1019 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7201 (mm) REVERT: B 29 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7645 (mtm110) REVERT: B 71 ASP cc_start: 0.8073 (m-30) cc_final: 0.7570 (p0) REVERT: B 73 SER cc_start: 0.8781 (m) cc_final: 0.7965 (m) REVERT: B 195 ASP cc_start: 0.8228 (m-30) cc_final: 0.7665 (t0) REVERT: B 269 ILE cc_start: 0.8178 (mm) cc_final: 0.7945 (mm) REVERT: B 334 VAL cc_start: 0.8899 (t) cc_final: 0.8659 (p) REVERT: B 356 ILE cc_start: 0.8489 (mm) cc_final: 0.8210 (mt) REVERT: B 399 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6585 (mt-10) REVERT: B 401 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: B 457 ASP cc_start: 0.8105 (t0) cc_final: 0.7803 (t0) REVERT: B 555 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 591 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8496 (ttmm) REVERT: B 642 LYS cc_start: 0.8304 (tttp) cc_final: 0.8103 (ttpt) REVERT: B 813 ASP cc_start: 0.7854 (p0) cc_final: 0.7541 (p0) REVERT: C 24 LYS cc_start: 0.8906 (tptp) cc_final: 0.8545 (tptp) REVERT: C 73 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7672 (mpp) REVERT: C 98 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8296 (mtt-85) REVERT: C 130 TYR cc_start: 0.8790 (m-80) cc_final: 0.8254 (m-80) REVERT: C 184 TYR cc_start: 0.8260 (t80) cc_final: 0.7971 (t80) REVERT: C 228 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7547 (mmm) REVERT: C 259 ASN cc_start: 0.8758 (t0) cc_final: 0.8508 (t0) REVERT: C 347 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 368 ASP cc_start: 0.8042 (t0) cc_final: 0.7550 (t0) REVERT: C 447 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7887 (tt) REVERT: C 458 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: D 1044 GLN cc_start: 0.7138 (tt0) cc_final: 0.6004 (pt0) REVERT: D 1061 LYS cc_start: 0.7411 (tptt) cc_final: 0.7147 (tptt) REVERT: D 1121 MET cc_start: 0.8027 (mmp) cc_final: 0.7708 (mmt) REVERT: D 1245 LEU cc_start: 0.7781 (tp) cc_final: 0.7502 (tm) REVERT: D 1263 LEU cc_start: 0.7928 (pp) cc_final: 0.7582 (mp) outliers start: 84 outliers final: 52 residues processed: 440 average time/residue: 0.5630 time to fit residues: 286.5253 Evaluate side-chains 457 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 395 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 95 optimal weight: 0.9990 chunk 235 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 206 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS B 814 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111030 restraints weight = 36502.174| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.44 r_work: 0.3296 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25085 Z= 0.147 Angle : 0.626 13.705 34408 Z= 0.324 Chirality : 0.044 0.207 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.600 169.839 4306 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.03 % Allowed : 16.06 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.55 (0.15), residues: 2831 helix: 1.32 (0.17), residues: 935 sheet: -0.01 (0.20), residues: 672 loop : -1.98 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.026 0.001 TYR D 978 PHE 0.019 0.002 PHE A 207 TRP 0.027 0.001 TRP B 677 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (25082) covalent geometry : angle 0.61764 / 0.32 (34399) hydrogen bonds : bond 0.04834 / 3.19 ( 1022) hydrogen bonds : angle 4.51929 / 3.15 ( 2869) metal coordination : bond 0.00592 / 0.29 ( 3) metal coordination : angle 6.30810 / 2.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 396 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8769 (t80) cc_final: 0.8492 (t80) REVERT: A 65 GLU cc_start: 0.8331 (pm20) cc_final: 0.7787 (pp20) REVERT: A 81 GLU cc_start: 0.7259 (pp20) cc_final: 0.6807 (pp20) REVERT: A 227 GLU cc_start: 0.8517 (mp0) cc_final: 0.8159 (mp0) REVERT: A 471 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (t) REVERT: A 475 VAL cc_start: 0.8744 (p) cc_final: 0.8432 (t) REVERT: A 521 GLU cc_start: 0.7963 (pm20) cc_final: 0.7677 (pm20) REVERT: A 567 LYS cc_start: 0.8437 (mttm) cc_final: 0.8220 (mtpm) REVERT: A 602 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8471 (ttt180) REVERT: A 666 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: A 743 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8115 (mp0) REVERT: A 789 GLU cc_start: 0.7603 (tp30) cc_final: 0.7184 (tp30) REVERT: A 916 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 976 LYS cc_start: 0.8783 (tptp) cc_final: 0.8394 (tppp) REVERT: A 1001 MET cc_start: 0.5758 (mmm) cc_final: 0.5347 (mpm) REVERT: A 1019 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 18 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (m) REVERT: B 29 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7693 (mtm110) REVERT: B 71 ASP cc_start: 0.8095 (m-30) cc_final: 0.7544 (p0) REVERT: B 73 SER cc_start: 0.8758 (m) cc_final: 0.8031 (p) REVERT: B 193 GLN cc_start: 0.7785 (pp30) cc_final: 0.7487 (pp30) REVERT: B 195 ASP cc_start: 0.8165 (m-30) cc_final: 0.7682 (t0) REVERT: B 334 VAL cc_start: 0.8899 (t) cc_final: 0.8671 (p) REVERT: B 356 ILE cc_start: 0.8438 (mm) cc_final: 0.8150 (mt) REVERT: B 399 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6600 (mt-10) REVERT: B 401 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: B 457 ASP cc_start: 0.8074 (t0) cc_final: 0.7784 (t0) REVERT: B 555 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8042 (p) REVERT: B 591 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8511 (ttmm) REVERT: B 813 ASP cc_start: 0.7861 (p0) cc_final: 0.7539 (p0) REVERT: C 24 LYS cc_start: 0.8875 (tptp) cc_final: 0.8513 (tptp) REVERT: C 98 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8299 (mtt-85) REVERT: C 130 TYR cc_start: 0.8771 (m-80) cc_final: 0.8167 (m-80) REVERT: C 184 TYR cc_start: 0.8221 (t80) cc_final: 0.7956 (t80) REVERT: C 347 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: C 368 ASP cc_start: 0.8001 (t0) cc_final: 0.7582 (t0) REVERT: C 447 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7818 (tt) REVERT: C 458 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: D 1058 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7519 (tm-30) REVERT: D 1061 LYS cc_start: 0.7418 (tptt) cc_final: 0.7132 (tptt) REVERT: D 1108 ASN cc_start: 0.6676 (p0) cc_final: 0.5061 (t160) REVERT: D 1121 MET cc_start: 0.8066 (mmp) cc_final: 0.7745 (mmt) REVERT: D 1245 LEU cc_start: 0.7768 (tp) cc_final: 0.7481 (tm) REVERT: D 1263 LEU cc_start: 0.7923 (pp) cc_final: 0.7580 (mp) outliers start: 76 outliers final: 46 residues processed: 432 average time/residue: 0.5696 time to fit residues: 284.6564 Evaluate side-chains 440 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 385 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 911 GLN Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1042 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 106 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 213 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS B 814 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 495 GLN D1059 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110349 restraints weight = 36536.715| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.45 r_work: 0.3289 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25085 Z= 0.193 Angle : 0.672 18.624 34408 Z= 0.345 Chirality : 0.046 0.390 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.577 170.517 4306 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.07 % Allowed : 16.42 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2831 helix: 1.28 (0.17), residues: 934 sheet: -0.07 (0.20), residues: 678 loop : -1.99 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.016 0.002 TYR C 122 PHE 0.022 0.002 PHE A 207 TRP 0.028 0.002 TRP B 677 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (25082) covalent geometry : angle 0.66375 / 0.34 (34399) hydrogen bonds : bond 0.05252 / 3.46 ( 1022) hydrogen bonds : angle 4.56580 / 3.17 ( 2869) metal coordination : bond 0.00678 / 0.34 ( 3) metal coordination : angle 6.66932 / 2.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 381 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8773 (t80) cc_final: 0.8503 (t80) REVERT: A 65 GLU cc_start: 0.8329 (pm20) cc_final: 0.7786 (pp20) REVERT: A 81 GLU cc_start: 0.7257 (pp20) cc_final: 0.6797 (pp20) REVERT: A 227 GLU cc_start: 0.8534 (mp0) cc_final: 0.8133 (mp0) REVERT: A 471 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8236 (t) REVERT: A 475 VAL cc_start: 0.8722 (p) cc_final: 0.8408 (t) REVERT: A 521 GLU cc_start: 0.7957 (pm20) cc_final: 0.7652 (pm20) REVERT: A 567 LYS cc_start: 0.8450 (mttm) cc_final: 0.8227 (mtpm) REVERT: A 602 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8453 (ttt180) REVERT: A 743 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8105 (mp0) REVERT: A 789 GLU cc_start: 0.7616 (tp30) cc_final: 0.7191 (tp30) REVERT: A 827 MET cc_start: 0.8107 (mtm) cc_final: 0.7907 (mtp) REVERT: A 916 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 976 LYS cc_start: 0.8786 (tptp) cc_final: 0.8398 (tppp) REVERT: A 1019 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7171 (mm) REVERT: B 18 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 29 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7693 (mtm110) REVERT: B 71 ASP cc_start: 0.8132 (m-30) cc_final: 0.7577 (p0) REVERT: B 73 SER cc_start: 0.8726 (m) cc_final: 0.7974 (p) REVERT: B 195 ASP cc_start: 0.8171 (m-30) cc_final: 0.7668 (t0) REVERT: B 334 VAL cc_start: 0.8900 (t) cc_final: 0.8663 (p) REVERT: B 356 ILE cc_start: 0.8480 (mm) cc_final: 0.8192 (mt) REVERT: B 399 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6576 (mt-10) REVERT: B 401 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: B 457 ASP cc_start: 0.8112 (t0) cc_final: 0.7804 (t0) REVERT: B 555 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8043 (p) REVERT: B 591 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8508 (ttmm) REVERT: B 813 ASP cc_start: 0.7849 (p0) cc_final: 0.7521 (p0) REVERT: C 24 LYS cc_start: 0.8881 (tptp) cc_final: 0.8517 (tptp) REVERT: C 73 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7632 (mpp) REVERT: C 98 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8338 (mtt-85) REVERT: C 130 TYR cc_start: 0.8777 (m-80) cc_final: 0.8226 (m-80) REVERT: C 184 TYR cc_start: 0.8235 (t80) cc_final: 0.7937 (t80) REVERT: C 228 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: C 347 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: C 368 ASP cc_start: 0.8037 (t0) cc_final: 0.7603 (t0) REVERT: C 447 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (tt) REVERT: C 458 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 1061 LYS cc_start: 0.7399 (tptt) cc_final: 0.7118 (tptt) REVERT: D 1108 ASN cc_start: 0.6702 (p0) cc_final: 0.5135 (t160) REVERT: D 1121 MET cc_start: 0.8058 (mmp) cc_final: 0.7740 (mmt) REVERT: D 1263 LEU cc_start: 0.7884 (pp) cc_final: 0.7550 (mp) outliers start: 77 outliers final: 44 residues processed: 419 average time/residue: 0.5396 time to fit residues: 261.0371 Evaluate side-chains 438 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1003 GLU Chi-restraints excluded: chain D residue 1048 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 276 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 239 optimal weight: 0.4980 chunk 201 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 198 GLN B 371 ASN B 437 HIS B 593 HIS B 814 HIS C 495 GLN D1015 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111413 restraints weight = 36251.046| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.42 r_work: 0.3298 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25085 Z= 0.158 Angle : 0.661 18.460 34408 Z= 0.337 Chirality : 0.045 0.453 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.523 171.125 4306 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.43 % Allowed : 17.34 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2831 helix: 1.31 (0.17), residues: 936 sheet: -0.05 (0.20), residues: 684 loop : -1.96 (0.16), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.015 0.001 TYR A 416 PHE 0.020 0.002 PHE A 207 TRP 0.025 0.002 TRP B 677 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (25082) covalent geometry : angle 0.65345 / 0.34 (34399) hydrogen bonds : bond 0.04823 / 3.18 ( 1022) hydrogen bonds : angle 4.51600 / 3.14 ( 2869) metal coordination : bond 0.00605 / 0.30 ( 3) metal coordination : angle 6.19853 / 2.63 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5662 Ramachandran restraints generated. 2831 Oldfield, 0 Emsley, 2831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 386 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8751 (t80) cc_final: 0.8492 (t80) REVERT: A 65 GLU cc_start: 0.8293 (pm20) cc_final: 0.7759 (pp20) REVERT: A 81 GLU cc_start: 0.7188 (pp20) cc_final: 0.6717 (pp20) REVERT: A 227 GLU cc_start: 0.8510 (mp0) cc_final: 0.8152 (mp0) REVERT: A 471 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 475 VAL cc_start: 0.8721 (p) cc_final: 0.8406 (t) REVERT: A 521 GLU cc_start: 0.7940 (pm20) cc_final: 0.7631 (pm20) REVERT: A 567 LYS cc_start: 0.8431 (mttm) cc_final: 0.8205 (mtpm) REVERT: A 602 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8468 (ttt180) REVERT: A 743 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8090 (mp0) REVERT: A 789 GLU cc_start: 0.7631 (tp30) cc_final: 0.7215 (tp30) REVERT: A 827 MET cc_start: 0.8108 (mtm) cc_final: 0.7891 (mtp) REVERT: A 916 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 976 LYS cc_start: 0.8823 (tptp) cc_final: 0.8417 (tppp) REVERT: A 1019 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7170 (mm) REVERT: B 18 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8239 (m) REVERT: B 22 LEU cc_start: 0.8798 (tp) cc_final: 0.8580 (tt) REVERT: B 29 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7695 (mtm110) REVERT: B 71 ASP cc_start: 0.8154 (m-30) cc_final: 0.7559 (p0) REVERT: B 73 SER cc_start: 0.8718 (m) cc_final: 0.7971 (p) REVERT: B 195 ASP cc_start: 0.8167 (m-30) cc_final: 0.7691 (t0) REVERT: B 198 GLN cc_start: 0.8672 (mt0) cc_final: 0.8402 (mt0) REVERT: B 334 VAL cc_start: 0.8891 (t) cc_final: 0.8648 (p) REVERT: B 356 ILE cc_start: 0.8441 (mm) cc_final: 0.8153 (mt) REVERT: B 399 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6576 (mt-10) REVERT: B 401 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: B 457 ASP cc_start: 0.8083 (t0) cc_final: 0.7789 (t0) REVERT: B 555 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8050 (p) REVERT: B 591 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8501 (ttmm) REVERT: B 813 ASP cc_start: 0.7837 (p0) cc_final: 0.7503 (p0) REVERT: C 24 LYS cc_start: 0.8882 (tptp) cc_final: 0.8507 (tptp) REVERT: C 98 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8333 (mtt-85) REVERT: C 130 TYR cc_start: 0.8773 (m-80) cc_final: 0.8211 (m-80) REVERT: C 184 TYR cc_start: 0.8221 (t80) cc_final: 0.7929 (t80) REVERT: C 228 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7408 (mmm) REVERT: C 347 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 368 ASP cc_start: 0.8035 (t0) cc_final: 0.7613 (t0) REVERT: C 447 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 458 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: C 475 LEU cc_start: 0.8859 (tp) cc_final: 0.8657 (tt) REVERT: D 1061 LYS cc_start: 0.7421 (tptt) cc_final: 0.7166 (tptt) REVERT: D 1108 ASN cc_start: 0.6646 (p0) cc_final: 0.5319 (t160) REVERT: D 1121 MET cc_start: 0.8058 (mmp) cc_final: 0.7733 (mmt) REVERT: D 1263 LEU cc_start: 0.7886 (pp) cc_final: 0.7571 (mp) outliers start: 61 outliers final: 38 residues processed: 416 average time/residue: 0.5745 time to fit residues: 276.0964 Evaluate side-chains 432 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 384 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1230 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain D residue 1243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 225 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS B 814 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.153294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110737 restraints weight = 36325.818| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.51 r_work: 0.3295 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25085 Z= 0.172 Angle : 0.669 16.979 34408 Z= 0.341 Chirality : 0.046 0.449 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.493 171.709 4306 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.35 % Allowed : 17.50 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2831 helix: 1.33 (0.17), residues: 935 sheet: -0.03 (0.20), residues: 684 loop : -1.97 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 306 TYR 0.015 0.002 TYR A 416 PHE 0.021 0.002 PHE A 278 TRP 0.016 0.002 TRP B 215 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (25082) covalent geometry : angle 0.66074 / 0.34 (34399) hydrogen bonds : bond 0.05031 / 3.31 ( 1022) hydrogen bonds : angle 4.52896 / 3.15 ( 2869) metal coordination : bond 0.00611 / 0.31 ( 3) metal coordination : angle 6.43397 / 2.77 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10741.88 seconds wall clock time: 183 minutes 1.38 seconds (10981.38 seconds total)