Starting phenix.real_space_refine on Sun Jan 26 07:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptx_17924/01_2025/8ptx_17924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptx_17924/01_2025/8ptx_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_17924/01_2025/8ptx_17924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptx_17924/01_2025/8ptx_17924.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptx_17924/01_2025/8ptx_17924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptx_17924/01_2025/8ptx_17924.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 15.33, per 1000 atoms: 0.63 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: 6.40 Conformation dependent library (CDL) restraints added in 2.9 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: 8.83 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: 14.02 Time building geometry restraints manager: 7.29 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=" 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 bond pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.39e-02 5.18e+03 6.80e+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: 3731 0.103 - 0.206: 164 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: 0.000 Normalize map: mean=0, sd=1: 9.510 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: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 69.590 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 25082 Z= 0.243 Angle : 0.662 26.071 34399 Z= 0.388 Chirality : 0.049 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 TRP 0.020 0.001 TRP A 224 HIS 0.008 0.001 HIS A 656 PHE 0.018 0.002 PHE A1022 TYR 0.027 0.001 TYR C 122 ARG 0.007 0.000 ARG D1011 *********************** 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 : 2.972 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: 0.7155 (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: 0.7773 (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: 0.6659 (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: 1.5851 time to fit residues: 819.7092 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 : 2.929 ------------------------------------------------------------------------------- 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 244 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 0.1980 chunk 263 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 271 ASN A 329 HIS ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN A 751 ASN A 888 ASN A 972 ASN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 188 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 662 ASN B 776 GLN B 814 HIS 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 = 0.4009 r_free = 0.4009 target = 0.152411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110816 restraints weight = 37106.643| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.36 r_work: 0.3301 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25082 Z= 0.272 Angle : 0.642 8.955 34399 Z= 0.333 Chirality : 0.045 0.209 3907 Planarity : 0.005 0.053 4126 Dihedral : 15.173 156.778 4311 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.91 % Allowed : 9.29 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2831 helix: 1.31 (0.17), residues: 924 sheet: 0.23 (0.20), residues: 627 loop : -1.90 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 215 HIS 0.010 0.001 HIS D 995 PHE 0.030 0.002 PHE D1131 TYR 0.015 0.002 TYR B 564 ARG 0.007 0.000 ARG B 306 *********************** 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 460 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 412 time to evaluate : 2.337 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: 0.7187 (pp20) cc_final: 0.6627 (pp20) REVERT: A 110 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 187 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 227 GLU cc_start: 0.8332 (mp0) cc_final: 0.8086 (mp0) REVERT: A 521 GLU cc_start: 0.8047 (pm20) cc_final: 0.7781 (pm20) REVERT: A 567 LYS cc_start: 0.8442 (mttm) cc_final: 0.8212 (mtpm) REVERT: A 582 LEU cc_start: 0.9029 (mp) cc_final: 0.8822 (mt) REVERT: A 602 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8458 (ttt180) REVERT: A 666 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7595 (mtm-85) REVERT: A 690 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8206 (mttp) REVERT: A 743 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8048 (mp0) REVERT: A 789 GLU cc_start: 0.7342 (tp30) cc_final: 0.6908 (tp30) REVERT: A 916 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 976 LYS cc_start: 0.8765 (tptp) cc_final: 0.8467 (tppp) REVERT: A 1001 MET cc_start: 0.5568 (mmm) cc_final: 0.5089 (mpm) REVERT: B 29 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7627 (mtm110) REVERT: B 39 SER cc_start: 0.8584 (m) cc_final: 0.8378 (t) REVERT: B 71 ASP cc_start: 0.8006 (m-30) cc_final: 0.7680 (p0) REVERT: B 73 SER cc_start: 0.8816 (m) cc_final: 0.8118 (p) REVERT: B 193 GLN cc_start: 0.7304 (pp30) cc_final: 0.6874 (pp30) REVERT: B 195 ASP cc_start: 0.8189 (m-30) cc_final: 0.7556 (t0) REVERT: B 198 GLN cc_start: 0.8663 (mt0) cc_final: 0.8419 (mt0) REVERT: B 261 THR cc_start: 0.8566 (p) cc_final: 0.8290 (t) REVERT: B 399 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6589 (mt-10) REVERT: B 401 GLU cc_start: 0.7736 (mp0) cc_final: 0.6805 (mp0) REVERT: B 423 GLN cc_start: 0.5878 (tm-30) cc_final: 0.5647 (tm-30) REVERT: B 457 ASP cc_start: 0.8101 (t0) cc_final: 0.7747 (t0) REVERT: B 591 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8281 (ttmm) REVERT: B 615 LEU cc_start: 0.8010 (mm) cc_final: 0.7807 (mm) REVERT: B 642 LYS cc_start: 0.8224 (tttm) cc_final: 0.7988 (ttpt) REVERT: C 24 LYS cc_start: 0.8904 (tptp) cc_final: 0.8526 (tptp) REVERT: C 98 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8303 (mtt-85) REVERT: C 130 TYR cc_start: 0.8800 (m-80) cc_final: 0.8249 (m-80) REVERT: C 248 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7047 (mt0) REVERT: C 347 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: C 368 ASP cc_start: 0.8138 (t0) cc_final: 0.7626 (t0) REVERT: C 380 HIS cc_start: 0.7756 (m-70) cc_final: 0.7508 (m-70) REVERT: C 458 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: D 1044 GLN cc_start: 0.6901 (tt0) cc_final: 0.6069 (mt0) REVERT: D 1061 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6979 (mmmt) REVERT: D 1121 MET cc_start: 0.7315 (mmp) cc_final: 0.6898 (mmt) REVERT: D 1263 LEU cc_start: 0.7944 (pp) cc_final: 0.7515 (mp) outliers start: 48 outliers final: 16 residues processed: 429 average time/residue: 1.4910 time to fit residues: 732.6127 Evaluate side-chains 417 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 395 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 ARG 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 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain B residue 5 VAL 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 717 LEU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 248 GLN 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 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.0040 chunk 249 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 814 HIS C 199 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111161 restraints weight = 36745.075| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.40 r_work: 0.3301 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25082 Z= 0.247 Angle : 0.607 9.467 34399 Z= 0.316 Chirality : 0.044 0.199 3907 Planarity : 0.005 0.066 4126 Dihedral : 14.853 158.312 4306 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.55 % Allowed : 11.68 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2831 helix: 1.39 (0.17), residues: 924 sheet: 0.26 (0.20), residues: 627 loop : -1.89 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 215 HIS 0.006 0.001 HIS B 359 PHE 0.020 0.002 PHE A 207 TYR 0.014 0.001 TYR A 416 ARG 0.011 0.000 ARG A 525 *********************** 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 467 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 403 time to evaluate : 2.365 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: 0.8757 (t80) cc_final: 0.8498 (t80) REVERT: A 81 GLU cc_start: 0.7386 (pp20) cc_final: 0.6901 (tm-30) REVERT: A 187 SER cc_start: 0.8508 (t) cc_final: 0.8281 (p) REVERT: A 227 GLU cc_start: 0.8402 (mp0) cc_final: 0.8143 (mp0) REVERT: A 471 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (t) REVERT: A 521 GLU cc_start: 0.8021 (pm20) cc_final: 0.7708 (pm20) REVERT: A 525 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7882 (mtp85) REVERT: A 567 LYS cc_start: 0.8458 (mttm) cc_final: 0.8250 (mtpm) REVERT: A 602 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8479 (ttt180) REVERT: A 666 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7571 (mtm-85) REVERT: A 690 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8221 (mttp) REVERT: A 743 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8048 (mp0) REVERT: A 789 GLU cc_start: 0.7401 (tp30) cc_final: 0.6953 (tp30) REVERT: A 916 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 976 LYS cc_start: 0.8780 (tptp) cc_final: 0.8454 (tppp) REVERT: A 1001 MET cc_start: 0.5600 (mmm) cc_final: 0.5173 (mpm) REVERT: B 29 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7594 (mtm110) REVERT: B 39 SER cc_start: 0.8601 (m) cc_final: 0.8379 (t) REVERT: B 71 ASP cc_start: 0.8018 (m-30) cc_final: 0.7660 (p0) REVERT: B 73 SER cc_start: 0.8821 (m) cc_final: 0.8139 (p) REVERT: B 193 GLN cc_start: 0.7232 (pp30) cc_final: 0.6722 (pp30) REVERT: B 195 ASP cc_start: 0.8256 (m-30) cc_final: 0.7595 (t0) REVERT: B 198 GLN cc_start: 0.8699 (mt0) cc_final: 0.8348 (mt0) REVERT: B 261 THR cc_start: 0.8612 (p) cc_final: 0.8311 (t) REVERT: B 269 ILE cc_start: 0.8105 (mm) cc_final: 0.7818 (mm) REVERT: B 302 GLN cc_start: 0.7866 (mp10) cc_final: 0.7456 (mp10) REVERT: B 334 VAL cc_start: 0.8872 (t) cc_final: 0.8583 (p) REVERT: B 356 ILE cc_start: 0.8389 (mm) cc_final: 0.8123 (mt) REVERT: B 399 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6602 (mt-10) REVERT: B 401 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: B 457 ASP cc_start: 0.8106 (t0) cc_final: 0.7772 (t0) REVERT: B 642 LYS cc_start: 0.8272 (tttm) cc_final: 0.8017 (ttpt) REVERT: C 24 LYS cc_start: 0.8891 (tptp) cc_final: 0.8522 (tptp) REVERT: C 98 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8312 (mtt-85) REVERT: C 130 TYR cc_start: 0.8802 (m-80) cc_final: 0.8216 (m-80) REVERT: C 163 ASP cc_start: 0.7809 (t0) cc_final: 0.7593 (t0) REVERT: C 228 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7485 (mmm) REVERT: C 248 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: C 347 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: C 368 ASP cc_start: 0.8095 (t0) cc_final: 0.7586 (t0) REVERT: C 380 HIS cc_start: 0.7821 (m-70) cc_final: 0.7576 (m-70) REVERT: C 458 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 1044 GLN cc_start: 0.6873 (tt0) cc_final: 0.5672 (pt0) REVERT: D 1121 MET cc_start: 0.7836 (mmp) cc_final: 0.7548 (mmt) REVERT: D 1124 LEU cc_start: 0.8717 (tm) cc_final: 0.8460 (pp) REVERT: D 1263 LEU cc_start: 0.7963 (pp) cc_final: 0.7599 (mp) outliers start: 64 outliers final: 32 residues processed: 428 average time/residue: 1.4425 time to fit residues: 707.8547 Evaluate side-chains 419 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 380 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 145 GLU 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 489 GLN 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 872 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain B residue 5 VAL 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 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 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 135 MET Chi-restraints excluded: chain C residue 228 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 109 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 238 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 814 HIS D 963 ASN ** D1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110869 restraints weight = 37048.358| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.45 r_work: 0.3302 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25082 Z= 0.256 Angle : 0.602 8.550 34399 Z= 0.314 Chirality : 0.044 0.193 3907 Planarity : 0.005 0.060 4126 Dihedral : 14.729 162.353 4306 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.87 % Allowed : 13.27 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2831 helix: 1.41 (0.17), residues: 931 sheet: 0.23 (0.20), residues: 642 loop : -1.91 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 215 HIS 0.006 0.001 HIS B 359 PHE 0.020 0.002 PHE A 207 TYR 0.015 0.001 TYR B 752 ARG 0.005 0.000 ARG A 525 *********************** 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 474 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 402 time to evaluate : 2.547 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 12 PHE cc_start: 0.8731 (t80) cc_final: 0.8470 (t80) REVERT: A 65 GLU cc_start: 0.8324 (pm20) cc_final: 0.7732 (pp20) REVERT: A 81 GLU cc_start: 0.7245 (pp20) cc_final: 0.6770 (pp20) REVERT: A 187 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 227 GLU cc_start: 0.8452 (mp0) cc_final: 0.8047 (mp0) REVERT: A 471 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8223 (t) REVERT: A 567 LYS cc_start: 0.8464 (mttm) cc_final: 0.8243 (mtpm) REVERT: A 602 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8483 (ttt180) REVERT: A 690 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8226 (mttp) REVERT: A 743 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8049 (mp0) REVERT: A 789 GLU cc_start: 0.7479 (tp30) cc_final: 0.7043 (tp30) REVERT: A 916 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7174 (tm-30) REVERT: A 976 LYS cc_start: 0.8807 (tptp) cc_final: 0.8452 (tppp) REVERT: A 1001 MET cc_start: 0.5623 (mmm) cc_final: 0.5213 (mpm) REVERT: A 1019 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 18 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8333 (t) REVERT: B 29 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7614 (mtm110) REVERT: B 39 SER cc_start: 0.8607 (m) cc_final: 0.8379 (t) REVERT: B 46 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 71 ASP cc_start: 0.8039 (m-30) cc_final: 0.7652 (p0) REVERT: B 73 SER cc_start: 0.8836 (m) cc_final: 0.8070 (p) REVERT: B 193 GLN cc_start: 0.7207 (pp30) cc_final: 0.6639 (pp30) REVERT: B 195 ASP cc_start: 0.8238 (m-30) cc_final: 0.7598 (t0) REVERT: B 198 GLN cc_start: 0.8726 (mt0) cc_final: 0.8342 (mt0) REVERT: B 261 THR cc_start: 0.8643 (p) cc_final: 0.8315 (t) REVERT: B 269 ILE cc_start: 0.8121 (mm) cc_final: 0.7864 (mm) REVERT: B 302 GLN cc_start: 0.7804 (mp10) cc_final: 0.7405 (mp10) REVERT: B 334 VAL cc_start: 0.8901 (t) cc_final: 0.8639 (p) REVERT: B 356 ILE cc_start: 0.8398 (mm) cc_final: 0.8135 (mt) REVERT: B 381 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 399 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6520 (mt-10) REVERT: B 401 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: B 423 GLN cc_start: 0.5545 (tm-30) cc_final: 0.5241 (tm-30) REVERT: B 457 ASP cc_start: 0.8110 (t0) cc_final: 0.7792 (t0) REVERT: B 555 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 642 LYS cc_start: 0.8279 (tttm) cc_final: 0.8038 (ttpt) REVERT: C 24 LYS cc_start: 0.8896 (tptp) cc_final: 0.8527 (tptp) REVERT: C 98 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8310 (mtt-85) REVERT: C 130 TYR cc_start: 0.8801 (m-80) cc_final: 0.8191 (m-80) REVERT: C 228 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7472 (mmm) REVERT: C 248 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7050 (mt0) REVERT: C 347 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: C 368 ASP cc_start: 0.8089 (t0) cc_final: 0.7560 (t0) REVERT: C 380 HIS cc_start: 0.7829 (m-70) cc_final: 0.7586 (m-70) REVERT: C 458 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: D 1044 GLN cc_start: 0.6869 (tt0) cc_final: 0.5793 (pt0) REVERT: D 1061 LYS cc_start: 0.7583 (tptt) cc_final: 0.7288 (tptt) REVERT: D 1121 MET cc_start: 0.7900 (mmp) cc_final: 0.7425 (mmt) REVERT: D 1263 LEU cc_start: 0.7954 (pp) cc_final: 0.7602 (mp) outliers start: 72 outliers final: 38 residues processed: 430 average time/residue: 1.4426 time to fit residues: 718.2201 Evaluate side-chains 440 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 390 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR 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 487 LYS 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 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 46 LEU Chi-restraints excluded: chain B residue 92 ILE 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 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 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 228 MET 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 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** 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 96 GLN B 194 ASN B 814 HIS D1015 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111562 restraints weight = 36913.428| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.46 r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25082 Z= 0.217 Angle : 0.586 8.437 34399 Z= 0.304 Chirality : 0.043 0.189 3907 Planarity : 0.004 0.059 4126 Dihedral : 14.646 166.623 4306 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.83 % Allowed : 13.83 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2831 helix: 1.49 (0.17), residues: 930 sheet: 0.25 (0.20), residues: 639 loop : -1.87 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 224 HIS 0.005 0.001 HIS B 359 PHE 0.019 0.002 PHE A 207 TYR 0.014 0.001 TYR A 416 ARG 0.011 0.000 ARG A 525 *********************** 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 468 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 397 time to evaluate : 2.940 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: 0.8719 (t80) cc_final: 0.8449 (t80) REVERT: A 65 GLU cc_start: 0.8332 (pm20) cc_final: 0.7747 (pp20) REVERT: A 81 GLU cc_start: 0.7343 (pp20) cc_final: 0.6860 (pp20) REVERT: A 471 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (t) REVERT: A 567 LYS cc_start: 0.8420 (mttm) cc_final: 0.8205 (mtpm) REVERT: A 602 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8508 (ttt180) REVERT: A 690 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8222 (mttp) REVERT: A 743 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8067 (mp0) REVERT: A 789 GLU cc_start: 0.7497 (tp30) cc_final: 0.7062 (tp30) REVERT: A 916 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 976 LYS cc_start: 0.8825 (tptp) cc_final: 0.8453 (tppp) REVERT: A 1001 MET cc_start: 0.5622 (mmm) cc_final: 0.5237 (mpm) REVERT: A 1019 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7234 (mm) REVERT: B 29 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7626 (mtm110) REVERT: B 39 SER cc_start: 0.8597 (m) cc_final: 0.8388 (t) REVERT: B 46 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 71 ASP cc_start: 0.8039 (m-30) cc_final: 0.7611 (p0) REVERT: B 73 SER cc_start: 0.8816 (m) cc_final: 0.8116 (p) REVERT: B 193 GLN cc_start: 0.7239 (pp30) cc_final: 0.6567 (pp30) REVERT: B 195 ASP cc_start: 0.8270 (m-30) cc_final: 0.7634 (t0) REVERT: B 198 GLN cc_start: 0.8725 (mt0) cc_final: 0.8325 (mt0) REVERT: B 334 VAL cc_start: 0.8918 (t) cc_final: 0.8668 (p) REVERT: B 356 ILE cc_start: 0.8397 (mm) cc_final: 0.8137 (mt) REVERT: B 399 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6621 (mt-10) REVERT: B 401 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: B 423 GLN cc_start: 0.5764 (tm-30) cc_final: 0.5511 (tm-30) REVERT: B 457 ASP cc_start: 0.8094 (t0) cc_final: 0.7812 (t0) REVERT: B 555 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8023 (p) REVERT: B 591 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8493 (ttmm) REVERT: B 623 SER cc_start: 0.8074 (m) cc_final: 0.7655 (t) REVERT: B 642 LYS cc_start: 0.8284 (tttm) cc_final: 0.8034 (ttpt) REVERT: C 24 LYS cc_start: 0.8899 (tptp) cc_final: 0.8524 (tptp) REVERT: C 98 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8307 (mtt-85) REVERT: C 130 TYR cc_start: 0.8801 (m-80) cc_final: 0.8176 (m-80) REVERT: C 198 SER cc_start: 0.8291 (p) cc_final: 0.7995 (p) REVERT: C 248 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: C 259 ASN cc_start: 0.8691 (t0) cc_final: 0.8487 (t0) REVERT: C 347 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: C 368 ASP cc_start: 0.8091 (t0) cc_final: 0.7569 (t0) REVERT: C 380 HIS cc_start: 0.7806 (m-70) cc_final: 0.7578 (m-70) REVERT: C 447 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7825 (tt) REVERT: C 458 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: D 1044 GLN cc_start: 0.6894 (tt0) cc_final: 0.5795 (pt0) REVERT: D 1061 LYS cc_start: 0.7623 (tptt) cc_final: 0.7194 (pttt) REVERT: D 1121 MET cc_start: 0.7994 (mmp) cc_final: 0.7629 (mmt) REVERT: D 1245 LEU cc_start: 0.7690 (tp) cc_final: 0.7413 (tm) REVERT: D 1263 LEU cc_start: 0.7929 (pp) cc_final: 0.7581 (mp) outliers start: 71 outliers final: 40 residues processed: 424 average time/residue: 1.4190 time to fit residues: 693.7322 Evaluate side-chains 439 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR 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 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 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 B residue 5 VAL Chi-restraints excluded: chain B residue 46 LEU 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 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 592 GLU 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 73 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 248 GLN 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 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 169 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 710 GLN A 751 ASN A 972 ASN A1044 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 814 HIS C 307 ASN D1127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110138 restraints weight = 36548.139| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.38 r_work: 0.3284 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25082 Z= 0.314 Angle : 0.628 12.360 34399 Z= 0.325 Chirality : 0.045 0.230 3907 Planarity : 0.005 0.061 4126 Dihedral : 14.588 166.803 4306 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.03 % Allowed : 14.35 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2831 helix: 1.47 (0.17), residues: 934 sheet: 0.07 (0.20), residues: 666 loop : -1.95 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 215 HIS 0.007 0.001 HIS B 359 PHE 0.022 0.002 PHE A 278 TYR 0.016 0.002 TYR A 416 ARG 0.007 0.000 ARG B 306 *********************** 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 475 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 399 time to evaluate : 2.577 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: 0.8746 (t80) cc_final: 0.8456 (t80) REVERT: A 65 GLU cc_start: 0.8347 (pm20) cc_final: 0.7786 (pp20) REVERT: A 81 GLU cc_start: 0.7336 (pp20) cc_final: 0.6834 (pp20) REVERT: A 227 GLU cc_start: 0.8409 (mp0) cc_final: 0.8028 (mp0) REVERT: A 471 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8277 (t) REVERT: A 521 GLU cc_start: 0.7986 (pm20) cc_final: 0.7614 (pm20) REVERT: A 567 LYS cc_start: 0.8438 (mttm) cc_final: 0.8223 (mtpm) REVERT: A 602 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8503 (ttt180) REVERT: A 690 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8231 (mttp) REVERT: A 743 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8103 (mp0) REVERT: A 789 GLU cc_start: 0.7562 (tp30) cc_final: 0.7135 (tp30) REVERT: A 916 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7231 (tm-30) REVERT: A 976 LYS cc_start: 0.8826 (tptp) cc_final: 0.8449 (tppp) REVERT: A 1001 MET cc_start: 0.5723 (mmm) cc_final: 0.5354 (mpm) REVERT: A 1019 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7223 (mm) REVERT: B 18 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (m) REVERT: B 29 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7643 (mtm110) REVERT: B 39 SER cc_start: 0.8632 (m) cc_final: 0.8387 (t) REVERT: B 46 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 71 ASP cc_start: 0.8055 (m-30) cc_final: 0.7615 (p0) REVERT: B 73 SER cc_start: 0.8793 (m) cc_final: 0.8043 (p) REVERT: B 193 GLN cc_start: 0.7283 (pp30) cc_final: 0.6965 (pp30) REVERT: B 195 ASP cc_start: 0.8281 (m-30) cc_final: 0.7656 (t0) REVERT: B 269 ILE cc_start: 0.8153 (mm) cc_final: 0.7920 (mm) REVERT: B 334 VAL cc_start: 0.8916 (t) cc_final: 0.8685 (p) REVERT: B 356 ILE cc_start: 0.8451 (mm) cc_final: 0.8179 (mt) REVERT: B 399 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6643 (mt-10) REVERT: B 401 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 457 ASP cc_start: 0.8140 (t0) cc_final: 0.7846 (t0) REVERT: B 555 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8046 (p) REVERT: B 591 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8504 (ttmm) REVERT: B 764 ASN cc_start: 0.6281 (t0) cc_final: 0.5912 (t0) REVERT: B 813 ASP cc_start: 0.7893 (p0) cc_final: 0.7592 (p0) REVERT: C 24 LYS cc_start: 0.8899 (tptp) cc_final: 0.8539 (tptp) REVERT: C 98 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8296 (mtt-85) REVERT: C 130 TYR cc_start: 0.8804 (m-80) cc_final: 0.8215 (m-80) REVERT: C 184 TYR cc_start: 0.8267 (t80) cc_final: 0.7973 (t80) REVERT: C 228 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: C 248 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: C 347 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 368 ASP cc_start: 0.8087 (t0) cc_final: 0.7592 (t0) REVERT: C 447 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7852 (tt) REVERT: C 458 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: D 1044 GLN cc_start: 0.7027 (tt0) cc_final: 0.5936 (pt0) REVERT: D 1061 LYS cc_start: 0.7685 (tptt) cc_final: 0.7444 (tptt) REVERT: D 1121 MET cc_start: 0.8020 (mmp) cc_final: 0.7676 (mmt) REVERT: D 1245 LEU cc_start: 0.7743 (tp) cc_final: 0.7462 (tm) REVERT: D 1263 LEU cc_start: 0.7914 (pp) cc_final: 0.7563 (mp) outliers start: 76 outliers final: 46 residues processed: 434 average time/residue: 1.4422 time to fit residues: 720.5861 Evaluate side-chains 447 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 389 time to evaluate : 2.772 ------------------------------------------------------------------------------- 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 478 ARG Chi-restraints excluded: chain A residue 538 MET 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 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 46 LEU 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 383 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 437 HIS 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 592 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 616 THR 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 51 LEU 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 188 ASN Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 248 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 168 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 282 optimal weight: 0.0870 chunk 259 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** 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 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 = 0.4032 r_free = 0.4032 target = 0.154647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111817 restraints weight = 36644.410| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.52 r_work: 0.3308 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25082 Z= 0.200 Angle : 0.591 10.223 34399 Z= 0.305 Chirality : 0.044 0.190 3907 Planarity : 0.004 0.061 4126 Dihedral : 14.513 167.957 4306 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.63 % Allowed : 15.46 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2831 helix: 1.52 (0.17), residues: 936 sheet: 0.11 (0.20), residues: 663 loop : -1.89 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 224 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.002 PHE A 207 TYR 0.013 0.001 TYR A 416 ARG 0.005 0.000 ARG A 525 *********************** 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 469 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 403 time to evaluate : 2.416 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: symmetry clash REVERT: A 12 PHE cc_start: 0.8749 (t80) cc_final: 0.8459 (t80) REVERT: A 65 GLU cc_start: 0.8287 (pm20) cc_final: 0.7731 (pp20) REVERT: A 81 GLU cc_start: 0.7253 (pp20) cc_final: 0.6791 (pp20) REVERT: A 471 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8219 (t) REVERT: A 521 GLU cc_start: 0.7974 (pm20) cc_final: 0.7617 (pm20) REVERT: A 567 LYS cc_start: 0.8437 (mttm) cc_final: 0.8212 (mtpm) REVERT: A 602 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8476 (ttt180) REVERT: A 690 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8252 (mttp) REVERT: A 743 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8094 (mp0) REVERT: A 789 GLU cc_start: 0.7601 (tp30) cc_final: 0.7178 (tp30) REVERT: A 916 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 976 LYS cc_start: 0.8797 (tptp) cc_final: 0.8409 (tppp) REVERT: A 1001 MET cc_start: 0.5669 (mmm) cc_final: 0.5339 (mpm) REVERT: A 1019 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7231 (mm) REVERT: B 18 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8207 (m) REVERT: B 29 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7683 (mtm110) REVERT: B 39 SER cc_start: 0.8628 (m) cc_final: 0.8399 (t) REVERT: B 46 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 71 ASP cc_start: 0.8082 (m-30) cc_final: 0.7555 (p0) REVERT: B 73 SER cc_start: 0.8756 (m) cc_final: 0.8058 (p) REVERT: B 193 GLN cc_start: 0.7380 (pp30) cc_final: 0.6742 (pp30) REVERT: B 195 ASP cc_start: 0.8269 (m-30) cc_final: 0.7683 (t0) REVERT: B 198 GLN cc_start: 0.8740 (mt0) cc_final: 0.8348 (mt0) REVERT: B 334 VAL cc_start: 0.8916 (t) cc_final: 0.8697 (p) REVERT: B 356 ILE cc_start: 0.8410 (mm) cc_final: 0.8125 (mt) REVERT: B 381 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 395 VAL cc_start: 0.9059 (t) cc_final: 0.8805 (m) REVERT: B 399 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 401 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: B 457 ASP cc_start: 0.8088 (t0) cc_final: 0.7791 (t0) REVERT: B 555 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8026 (p) REVERT: B 591 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8520 (ttmm) REVERT: B 764 ASN cc_start: 0.6395 (t0) cc_final: 0.6019 (t0) REVERT: B 813 ASP cc_start: 0.7888 (p0) cc_final: 0.7577 (p0) REVERT: C 24 LYS cc_start: 0.8877 (tptp) cc_final: 0.8503 (tptp) REVERT: C 98 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8287 (mtt-85) REVERT: C 130 TYR cc_start: 0.8781 (m-80) cc_final: 0.8183 (m-80) REVERT: C 184 TYR cc_start: 0.8206 (t80) cc_final: 0.7916 (t80) REVERT: C 228 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: C 248 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: C 259 ASN cc_start: 0.8665 (t0) cc_final: 0.8452 (t0) REVERT: C 347 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: C 368 ASP cc_start: 0.8034 (t0) cc_final: 0.7618 (t0) REVERT: C 447 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7786 (tt) REVERT: C 458 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: C 487 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8214 (mtt90) REVERT: D 1030 GLN cc_start: 0.7581 (mp-120) cc_final: 0.6725 (tm-30) REVERT: D 1044 GLN cc_start: 0.6912 (tt0) cc_final: 0.5894 (pt0) REVERT: D 1061 LYS cc_start: 0.7710 (tptt) cc_final: 0.7245 (pttt) REVERT: D 1077 GLU cc_start: 0.6057 (pm20) cc_final: 0.5739 (mp0) REVERT: D 1108 ASN cc_start: 0.6743 (p0) cc_final: 0.5214 (t160) REVERT: D 1245 LEU cc_start: 0.7735 (tp) cc_final: 0.7449 (tm) REVERT: D 1263 LEU cc_start: 0.7885 (pp) cc_final: 0.7555 (mt) outliers start: 66 outliers final: 35 residues processed: 433 average time/residue: 1.4395 time to fit residues: 716.7218 Evaluate side-chains 442 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 395 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 ARG 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 612 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 872 VAL 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 46 LEU 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 220 ARG 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 437 HIS 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 592 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 630 LEU 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 188 ASN Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 248 GLN 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 1042 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 21 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 221 optimal weight: 0.0060 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 276 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN A1238 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 425 GLN B 814 HIS D1231 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110640 restraints weight = 36335.572| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.44 r_work: 0.3288 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25082 Z= 0.289 Angle : 0.642 14.905 34399 Z= 0.329 Chirality : 0.046 0.323 3907 Planarity : 0.005 0.062 4126 Dihedral : 14.492 169.102 4306 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.83 % Allowed : 15.78 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2831 helix: 1.47 (0.17), residues: 934 sheet: 0.04 (0.20), residues: 670 loop : -1.93 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 677 HIS 0.008 0.001 HIS B 359 PHE 0.022 0.002 PHE A 278 TYR 0.016 0.002 TYR D 978 ARG 0.007 0.000 ARG B 306 *********************** 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 467 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 396 time to evaluate : 2.616 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: 0.8765 (t80) cc_final: 0.8484 (t80) REVERT: A 65 GLU cc_start: 0.8292 (pm20) cc_final: 0.7739 (pp20) REVERT: A 81 GLU cc_start: 0.7215 (pp20) cc_final: 0.6749 (pp20) REVERT: A 227 GLU cc_start: 0.8510 (mp0) cc_final: 0.8000 (mp0) REVERT: A 471 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8223 (t) REVERT: A 521 GLU cc_start: 0.7957 (pm20) cc_final: 0.7586 (pm20) REVERT: A 567 LYS cc_start: 0.8468 (mttm) cc_final: 0.8232 (mtpm) REVERT: A 602 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (ttt180) REVERT: A 743 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8103 (mp0) REVERT: A 789 GLU cc_start: 0.7629 (tp30) cc_final: 0.7200 (tp30) REVERT: A 916 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 976 LYS cc_start: 0.8829 (tptp) cc_final: 0.8436 (tppp) REVERT: A 1019 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7197 (mm) REVERT: B 18 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8282 (m) REVERT: B 29 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7683 (mtm110) REVERT: B 39 SER cc_start: 0.8659 (m) cc_final: 0.8410 (t) REVERT: B 46 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 71 ASP cc_start: 0.8092 (m-30) cc_final: 0.7551 (p0) REVERT: B 73 SER cc_start: 0.8750 (m) cc_final: 0.7985 (p) REVERT: B 193 GLN cc_start: 0.7365 (pp30) cc_final: 0.6979 (pp30) REVERT: B 195 ASP cc_start: 0.8275 (m-30) cc_final: 0.7685 (t0) REVERT: B 334 VAL cc_start: 0.8911 (t) cc_final: 0.8688 (p) REVERT: B 356 ILE cc_start: 0.8464 (mm) cc_final: 0.8175 (mt) REVERT: B 399 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6604 (mt-10) REVERT: B 401 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 457 ASP cc_start: 0.8075 (t0) cc_final: 0.7788 (t0) REVERT: B 555 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8042 (p) REVERT: B 591 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8510 (ttmm) REVERT: B 764 ASN cc_start: 0.6468 (t0) cc_final: 0.6249 (t0) REVERT: B 813 ASP cc_start: 0.7864 (p0) cc_final: 0.7539 (p0) REVERT: C 24 LYS cc_start: 0.8883 (tptp) cc_final: 0.8517 (tptp) REVERT: C 98 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8315 (mtt-85) REVERT: C 130 TYR cc_start: 0.8788 (m-80) cc_final: 0.8243 (m-80) REVERT: C 184 TYR cc_start: 0.8241 (t80) cc_final: 0.7941 (t80) REVERT: C 228 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: C 248 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7042 (mt0) REVERT: C 259 ASN cc_start: 0.8716 (t0) cc_final: 0.8478 (t0) REVERT: C 288 ASP cc_start: 0.8419 (t0) cc_final: 0.8217 (t0) REVERT: C 347 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: C 368 ASP cc_start: 0.8055 (t0) cc_final: 0.7627 (t0) REVERT: C 447 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7849 (tt) REVERT: C 458 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: C 475 LEU cc_start: 0.8874 (tp) cc_final: 0.8668 (tt) REVERT: D 1048 LEU cc_start: 0.7259 (mm) cc_final: 0.7033 (tm) REVERT: D 1061 LYS cc_start: 0.7746 (tptt) cc_final: 0.7537 (tptt) REVERT: D 1077 GLU cc_start: 0.6051 (pm20) cc_final: 0.5777 (mp0) REVERT: D 1108 ASN cc_start: 0.6857 (p0) cc_final: 0.5434 (t160) REVERT: D 1121 MET cc_start: 0.8071 (mmp) cc_final: 0.7535 (mmt) REVERT: D 1245 LEU cc_start: 0.7788 (tp) cc_final: 0.7502 (tm) REVERT: D 1263 LEU cc_start: 0.7882 (pp) cc_final: 0.7563 (mp) outliers start: 71 outliers final: 43 residues processed: 431 average time/residue: 1.4013 time to fit residues: 699.3422 Evaluate side-chains 450 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 ARG Chi-restraints excluded: chain A residue 538 MET 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 872 VAL 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 46 LEU 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 404 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 HIS 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 592 GLU Chi-restraints excluded: chain B residue 611 VAL 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 119 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 248 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 158 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 130 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 214 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 272 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 48 optimal weight: 0.0050 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 751 ASN A 972 ASN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4047 r_free = 0.4047 target = 0.155896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113654 restraints weight = 36542.472| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.42 r_work: 0.3338 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25082 Z= 0.160 Angle : 0.612 17.968 34399 Z= 0.310 Chirality : 0.043 0.183 3907 Planarity : 0.004 0.060 4126 Dihedral : 14.399 169.878 4306 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.35 % Allowed : 16.62 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2831 helix: 1.57 (0.17), residues: 934 sheet: 0.16 (0.20), residues: 665 loop : -1.86 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 224 HIS 0.003 0.001 HIS B 359 PHE 0.018 0.001 PHE B 450 TYR 0.013 0.001 TYR B 239 ARG 0.009 0.000 ARG D1253 *********************** 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 452 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 393 time to evaluate : 2.495 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: 0.8714 (t80) cc_final: 0.8452 (t80) REVERT: A 65 GLU cc_start: 0.8258 (pm20) cc_final: 0.7705 (pp20) REVERT: A 81 GLU cc_start: 0.7130 (pp20) cc_final: 0.6651 (pp20) REVERT: A 269 GLU cc_start: 0.8022 (tt0) cc_final: 0.7738 (tt0) REVERT: A 284 LYS cc_start: 0.7505 (tttt) cc_final: 0.7136 (mmmt) REVERT: A 471 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8196 (t) REVERT: A 475 VAL cc_start: 0.8689 (p) cc_final: 0.8386 (t) REVERT: A 521 GLU cc_start: 0.7943 (pm20) cc_final: 0.7548 (pm20) REVERT: A 559 SER cc_start: 0.8732 (m) cc_final: 0.8474 (p) REVERT: A 567 LYS cc_start: 0.8422 (mttm) cc_final: 0.8184 (mtpm) REVERT: A 743 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8035 (mp0) REVERT: A 789 GLU cc_start: 0.7613 (tp30) cc_final: 0.7166 (tp30) REVERT: A 916 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 976 LYS cc_start: 0.8805 (tptp) cc_final: 0.8405 (tppp) REVERT: A 1019 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7182 (mm) REVERT: B 18 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8177 (m) REVERT: B 29 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7663 (mtm110) REVERT: B 39 SER cc_start: 0.8616 (m) cc_final: 0.8391 (t) REVERT: B 46 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 52 THR cc_start: 0.8392 (t) cc_final: 0.8122 (m) REVERT: B 71 ASP cc_start: 0.8063 (m-30) cc_final: 0.7541 (p0) REVERT: B 73 SER cc_start: 0.8735 (m) cc_final: 0.8032 (p) REVERT: B 193 GLN cc_start: 0.7310 (pp30) cc_final: 0.6802 (pp30) REVERT: B 195 ASP cc_start: 0.8250 (m-30) cc_final: 0.7702 (t0) REVERT: B 198 GLN cc_start: 0.8728 (mt0) cc_final: 0.8306 (mt0) REVERT: B 315 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 356 ILE cc_start: 0.8363 (mm) cc_final: 0.8073 (mt) REVERT: B 399 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6610 (mt-10) REVERT: B 401 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: B 457 ASP cc_start: 0.8036 (t0) cc_final: 0.7791 (t0) REVERT: B 555 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8043 (p) REVERT: B 591 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8519 (ttmm) REVERT: B 813 ASP cc_start: 0.7852 (p0) cc_final: 0.7519 (p0) REVERT: C 24 LYS cc_start: 0.8853 (tptp) cc_final: 0.8461 (tptp) REVERT: C 28 GLU cc_start: 0.7846 (tt0) cc_final: 0.7558 (tt0) REVERT: C 98 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8265 (mtt-85) REVERT: C 130 TYR cc_start: 0.8764 (m-80) cc_final: 0.8157 (m-80) REVERT: C 184 TYR cc_start: 0.8160 (t80) cc_final: 0.7885 (t80) REVERT: C 259 ASN cc_start: 0.8699 (t0) cc_final: 0.8460 (t0) REVERT: C 347 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: C 368 ASP cc_start: 0.7986 (t0) cc_final: 0.7580 (t0) REVERT: C 447 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (tt) REVERT: C 458 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: D 1048 LEU cc_start: 0.7270 (mm) cc_final: 0.7066 (tm) REVERT: D 1061 LYS cc_start: 0.7733 (tptt) cc_final: 0.7511 (tptt) REVERT: D 1077 GLU cc_start: 0.6024 (pm20) cc_final: 0.5686 (mp0) REVERT: D 1108 ASN cc_start: 0.6789 (p0) cc_final: 0.5475 (t160) REVERT: D 1121 MET cc_start: 0.8036 (mmp) cc_final: 0.7511 (mmt) REVERT: D 1263 LEU cc_start: 0.7881 (pp) cc_final: 0.7554 (mp) outliers start: 59 outliers final: 34 residues processed: 422 average time/residue: 1.3738 time to fit residues: 671.1267 Evaluate side-chains 428 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 384 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 471 SER Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 566 THR 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 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 46 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 113 VAL 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 437 HIS 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 592 GLU Chi-restraints excluded: chain B residue 611 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 188 ASN 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 1330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 123 optimal weight: 0.2980 chunk 139 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 148 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** 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 814 HIS C 150 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112761 restraints weight = 36414.772| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.55 r_work: 0.3314 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25082 Z= 0.212 Angle : 0.638 16.736 34399 Z= 0.323 Chirality : 0.045 0.463 3907 Planarity : 0.004 0.061 4126 Dihedral : 14.358 170.370 4306 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.91 % Allowed : 17.54 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2831 helix: 1.60 (0.17), residues: 928 sheet: 0.14 (0.20), residues: 667 loop : -1.88 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 677 HIS 0.004 0.001 HIS B 359 PHE 0.018 0.002 PHE A 207 TYR 0.017 0.001 TYR C 122 ARG 0.009 0.000 ARG A 627 ********************** 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 446 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 2.680 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: 0.8733 (t80) cc_final: 0.8455 (t80) REVERT: A 65 GLU cc_start: 0.8261 (pm20) cc_final: 0.7715 (pp20) REVERT: A 81 GLU cc_start: 0.7182 (pp20) cc_final: 0.6668 (pp20) REVERT: A 269 GLU cc_start: 0.8080 (tt0) cc_final: 0.7778 (tt0) REVERT: A 284 LYS cc_start: 0.7409 (tttt) cc_final: 0.7049 (mmmt) REVERT: A 471 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (t) REVERT: A 475 VAL cc_start: 0.8722 (p) cc_final: 0.8414 (t) REVERT: A 521 GLU cc_start: 0.7959 (pm20) cc_final: 0.7546 (pm20) REVERT: A 559 SER cc_start: 0.8740 (m) cc_final: 0.8488 (p) REVERT: A 567 LYS cc_start: 0.8442 (mttm) cc_final: 0.8202 (mtpm) REVERT: A 666 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7437 (mtm-85) REVERT: A 743 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8065 (mp0) REVERT: A 789 GLU cc_start: 0.7668 (tp30) cc_final: 0.7241 (tp30) REVERT: A 827 MET cc_start: 0.7994 (mtm) cc_final: 0.7759 (mtp) REVERT: A 916 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 976 LYS cc_start: 0.8811 (tptp) cc_final: 0.8405 (tppp) REVERT: A 1019 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 18 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8208 (m) REVERT: B 29 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7679 (mtm110) REVERT: B 39 SER cc_start: 0.8622 (m) cc_final: 0.8394 (t) REVERT: B 46 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 71 ASP cc_start: 0.8107 (m-30) cc_final: 0.7533 (p0) REVERT: B 73 SER cc_start: 0.8725 (m) cc_final: 0.7959 (p) REVERT: B 193 GLN cc_start: 0.7339 (pp30) cc_final: 0.6825 (pp30) REVERT: B 195 ASP cc_start: 0.8234 (m-30) cc_final: 0.7697 (t0) REVERT: B 198 GLN cc_start: 0.8734 (mt0) cc_final: 0.8270 (mt0) REVERT: B 356 ILE cc_start: 0.8395 (mm) cc_final: 0.8109 (mt) REVERT: B 381 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 399 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6653 (mt-10) REVERT: B 401 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 457 ASP cc_start: 0.8070 (t0) cc_final: 0.7764 (t0) REVERT: B 555 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 591 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8518 (ttmm) REVERT: B 813 ASP cc_start: 0.7859 (p0) cc_final: 0.7541 (p0) REVERT: C 24 LYS cc_start: 0.8862 (tptp) cc_final: 0.8478 (tptp) REVERT: C 28 GLU cc_start: 0.7877 (tt0) cc_final: 0.7585 (tt0) REVERT: C 98 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8292 (mtt-85) REVERT: C 130 TYR cc_start: 0.8785 (m-80) cc_final: 0.8242 (m-80) REVERT: C 184 TYR cc_start: 0.8192 (t80) cc_final: 0.7925 (t80) REVERT: C 259 ASN cc_start: 0.8728 (t0) cc_final: 0.8482 (t0) REVERT: C 368 ASP cc_start: 0.8002 (t0) cc_final: 0.7587 (t0) REVERT: C 447 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7846 (tt) REVERT: C 458 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 1048 LEU cc_start: 0.7426 (mm) cc_final: 0.7207 (tm) REVERT: D 1061 LYS cc_start: 0.7758 (tptt) cc_final: 0.7526 (tptt) REVERT: D 1077 GLU cc_start: 0.6086 (pm20) cc_final: 0.5736 (mp0) REVERT: D 1108 ASN cc_start: 0.6928 (p0) cc_final: 0.5517 (t160) REVERT: D 1121 MET cc_start: 0.8005 (mmp) cc_final: 0.7249 (mmt) REVERT: D 1255 LEU cc_start: 0.7988 (tp) cc_final: 0.7729 (tp) REVERT: D 1263 LEU cc_start: 0.7871 (pp) cc_final: 0.7560 (mp) outliers start: 48 outliers final: 34 residues processed: 421 average time/residue: 1.3769 time to fit residues: 668.1650 Evaluate side-chains 436 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 471 SER Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 566 THR 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 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 46 LEU Chi-restraints excluded: chain B residue 92 ILE 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 404 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 HIS 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 592 GLU Chi-restraints excluded: chain B residue 611 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 124 THR Chi-restraints excluded: chain C residue 188 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** 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 814 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111183 restraints weight = 36360.404| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.49 r_work: 0.3303 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25082 Z= 0.279 Angle : 0.672 17.344 34399 Z= 0.341 Chirality : 0.046 0.456 3907 Planarity : 0.005 0.063 4126 Dihedral : 14.356 170.690 4306 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2831 helix: 1.54 (0.17), residues: 930 sheet: 0.09 (0.20), residues: 670 loop : -1.92 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 677 HIS 0.007 0.001 HIS B 359 PHE 0.020 0.002 PHE A 278 TYR 0.016 0.002 TYR A 416 ARG 0.011 0.000 ARG A 525 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: